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# Note fields in this file should be separated by *tabs* not spaces!
# format: nr<TAB>logic_name<TAB>description<TAB>display_label<TAB>displayable<TAB>web_data
#
1 ARRAY_LIV_GAMDETOX_0.25k_v1 Vectorbase probe alignments: LIV_GAMDETOX_0.25k_v1 OLIGO LIV_GAMDETOX_0.25k_v1 1
2 VirginiaTech_Insect_TE Transposable elements (TE) catalogued by Jake Tu, Virginia Tech VirginiaTech Insect TE 1
3 BACends Bacterial Artificial Chromosome (end sequences) of library clones that were used in the sequencing project are aligned to the genome using <a rel="external" href="http://www.sanger.ac.uk/Software/analysis/SSAHA2/">SSAHA2</a>. BAC ends 1 {'show_strands' => '1'}
4 BlastmiRNA Positions of miRNAs along the genome are shown. A BLASTN of genomic sequence regions against <a rel="external" href="http://microrna.sanger.ac.uk">miRBase</a> sequences is performed, and hits are clustered and filtered by E value. Aligned genomic sequence is then checked for possible secondary structure using RNAFold. If evidence is found that the genomic sequence could form a stable hairpin structure the locus is used to create a miRNA gene model. The resulting BLAST hit is used as supporting evidence for the miRNA gene. See <a href="/info/docs/genebuild/ncrna.html" class="cp-external">article</a>. miRBase miRNA 1 {'type'=>'rna'}
5 other_protein For various species, proteins from <a rel="external" href="http://uniprot.org">UniProtKB</a> are aligned to the genome with <a rel="external" href="http://genome.cshlp.org/cgi/content/abstract/14/5/988?maxtoshow=&HITS=10&hits=10&RESULTFORMAT=&andorexactfulltext=and&searchid=1&FIRSTINDEX=0&sortspec=relevance&volume=14&firstpage=988&resourcetype=HWCIT">GeneWise</a>. Other sp. prot. 1
6 cint_cdna Ciona intestinalis cDNA sequences from the <a rel="external" href="http://ghost.zool.kyoto-u.ac.jp/indexr1.html">Ghost Database</a> are aligned to the genome using <a rel="external" href="http://www.biomedcentral.com/1471-2105/6/31">Exonerate</a>. C.intestinalis cDNA 1 {'default' => {'contigviewbottom' => 'stack'},'type' => 'cdna'}
7 opossum_protein Opossum proteins from <a rel="external" href="http://uniprot.org">UniProtKB</a> are aligned to the genome using <a rel="external" href="http://genome.cshlp.org/cgi/content/abstract/14/5/988?maxtoshow=&HITS=10&hits=10&RESULTFORMAT=&andorexactfulltext=and&searchid=1&FIRSTINDEX=0&sortspec=relevance&volume=14&firstpage=988&resourcetype=HWCIT">GeneWise</a>. Opossum UniProtKB prot. 1
8 GadflyX FlyBase proteins aligned by WU-BlastX GadflyX 1
9 Superfamily Protein domains and motifs in the <a rel="external" href="http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6WK7-457CXWM-3D&_user=776054&_coverDate=11%2F02%2F2001&_rdoc=17&_fmt=high&_orig=browse&_srch=doc-info(%23toc%236899%232001%23996869995%23286382%23FLA%23display%23Volume)&_cdi=6899&_sort=d&_docanchor=&_ct=17&_acct=C000042238&_version=1&_urlVersion=0&_userid=776054&md5=a921e84cd71c59f75644aa28f3224b58">SUPERFAMILY</a> database. Superfamily domain 1 {'type'=>'domain'}
10 caenorhabditis_mrna Caenorhabditis ESTs aligned to the genome using BLAT (excluding C.elegans) caenorhabditis cDNA 1 {'type'=>'rna'}
11 est_exonerate 'Expressed Sequence Tags' (ESTs) are mapped onto the genome using <a rel="external" href="http://www.biomedcentral.com/1471-2105/6/31">Exonerate</a>. EST 1 {'type' => 'est','gene' => {'do_not_display' => 1}}
12 Dust Dust is a program that identifies low-complexity sequences (regions of the genome with a biased distribution of nucleotides, such as a repeat). The Dust module is widely used with BLAST to prevent 'sticky' regions from determining false hits. Low complexity (Dust) 1
13 FANTOM_GSC_PET These are short sequence tags from the start sites of polyA transcripts. These ditags were downloaded from the <a rel="external" href="http://fantom.gsc.riken.go.jp/">Riken Fantom</a> project and aligned to the genome using <a rel="external" href="http://www.biomedcentral.com/1471-2105/6/31">Exonerate</a>. Fantom GSC ditags 1
14 mouse_cdna Murine cDNAs from <a rel="external" href="http://www.ncbi.nlm.nih.gov/RefSeq/">NCBI RefSeq</a> and <a rel="external" href="http://www.ebi.ac.uk/embl/">EMBL</a> are aligned to the genome using <a rel="external" href="http://www.ebi.ac.uk/~guy/exonerate/">Exonerate</a>. Mouse RefSeq/EMBL cDNA 1 {'default' => {'contigviewbottom' => 'stack'},'type' => 'cdna'}
15 xlaevis_cDNA Xenopus laevis cDNAs from <a rel="external" href="http://www.ncbi.nlm.nih.gov/RefSeq/">NCBI RefSeq</a> and <a rel="external" href="http://www.ebi.ac.uk/embl/">EMBL</a> are aligned to the genome using <a rel="external" href="http://www.biomedcentral.com/1471-2105/6/31">Exonerate</a>. X.laevis cDNA 1 {'type' => 'cdna','default' => {'contigviewbottom' => 'stack'}}
16 Ab_initio_RepeatMask Interspersed repeats and low complexity sequence identified by <a rel="external" href="http://www.repeatmasker.org/">RepeatMasker</a> using ab initio repeat profiles specific to the species. Repeats (Recon) 1
17 AffyAlign Microarray probes from Affymetrix (and other manufacturers) are aligned to the genome by Ensembl, if probe sequences are provided. The mapping is a two-step procedure outlined <a href="/info/docs/microarray_probe_set_mapping.html">here</a>. Affymetrix probes 1
18 ensembl Transcripts were annotated by the Ensembl <a href="/info/docs/genebuild/genome_annotation.html" class="cp-external">genebuild</a>. Ensembl gene 1 {'colour_key' => '[biotype]_[status]','label_key' => '[text_label] [display_label]','default' => {'contigviewbottom' => 'transcript_label','contigviewtop' => 'gene_label','cytoview' => 'gene_label','MultiTop' => 'gene_label','MultiBottom' => 'collapsed_label','alignsliceviewbottom' => 'as_collapsed_label'},'multi_caption' => 'Ensembl genes, or Merged Ensembl and Havana genes'}
19 washu_contig Washington University Nematode clusters aligned by BLAT Washu. contig 1
20 human_cdna Human cDNAs from <a rel="external" href="http://www.ncbi.nlm.nih.gov/RefSeq/">NCBI RefSeq</a> and <a rel="external" href="http://www.ebi.ac.uk/embl/">EMBL</a> are aligned to the genome using <a rel="external" href="http://www.biomedcentral.com/1471-2105/6/31">Exonerate</a>. Human RefSeq/EMBL cDNA 1 {'default' => {'contigviewbottom' => 'stack'},'type' => 'cdna'}
21 tetraodon_est Tetraodon 'Expressed Sequence Tags' (ESTs) from <a rel="external" href="http://www.ncbi.nlm.nih.gov/dbEST/">dbEST</a> are aligned to the genome using <a rel="external" href="http://www.biomedcentral.com/1471-2105/6/31">Exonerate</a>. Tetraodon EST 1 {'type'=>'est'}
22 xtrop_cluster Xenopus laevis 'Expressed Sequence Tag Clusters' (ESTs) from <a rel="external" href="http://informatics.gurdon.cam.ac.uk/cgi-bin/public.exe">Gurdon Institute Xenopus tropicalis Full-Length Database</a> are aligned to the genome using <a rel="external" href="http://www.biomedcentral.com/1471-2105/6/31">Exonerate</a>. X.laevis EST cluster 1 {'type'=>'est'}
23 uncharacterized_change_in_nucleotide_seq Feature imported from <a rel="external" href="http://www.flybase.org">FlyBase</a>. Nuc. seq. change 1
24 est_5prim_savi Ciona savignyi 3' 'Expressed Sequence Tags' (ESTs) from uncorrected <a rel="external" href="http://ghost.zool.kyoto-u.ac.jp/indexr1.html">Ghost Database</a> data are aligned with <a rel="external" href="http://www.biomedcentral.com/1471-2105/6/31">Exonerate</a>. C.savignyi 5' EST 1 {'type'=>'est'}
25 CpG CpG islands are regions of nucleic acid sequence containing a high number of adjacent cytosine guanine pairs (along one strand). Usually unmethylated, they are associated with promoters and regulatory regions. They are determined from the genomic sequence using a program written by G. Miklem, similar to <a rel="external" href="http://emboss.sourceforge.net/apps/cvs/emboss/apps/newcpgreport.html">newcpgreport</a> in the EMBOSS package. CpG islands 1
26 est_3prim_savi Ciona savignyi 3' 'Expressed Sequence Tags' (ESTs) from uncorrected <a rel="external" href="http://ghost.zool.kyoto-u.ac.jp/indexr1.html">Ghost Database</a> data are aligned with <a rel="external" href="http://www.biomedcentral.com/1471-2105/6/31">Exonerate</a>. C.savignyi 3' EST 1 {'type'=>'est'}
27 polyA_site Feature imported from <a rel="external" href="http://www.flybase.org">FlyBase</a>. PolyA Site 1
28 ARRAY_LIV_AEGDETOX_0.25k_v1 Liverpool University - detox array reporters ARRAY_LIV_AEGDETOX_0.25k_v1 1
29 regulatory_region Feature imported from <a rel="external" href="http://www.flybase.org">FlyBase</a>. Regulatory Region 1
30 GSTEN Genes were annotated by <a rel="external" href="http://www.genoscope.cns.fr/spip/">Genoscope</a>, combining evidence from <a rel="external" href="http://www1.imim.es/software/geneid/">Geneid</a>, <a rel="external" href="http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6WK7-45VGF7T-9&_user=776054&_rdoc=1&_fmt=&_orig=search&_sort=d&view=c&_version=1&_urlVersion=0&_userid=776054&md5=aa15a5f8122912c172ddb9dd15b237dc">Genscan</a>, <a rel="external" href="http://genome.cshlp.org/cgi/content/abstract/14/5/988?maxtoshow=&HITS=10&hits=10&RESULTFORMAT=&andorexactfulltext=and&searchid=1&FIRSTINDEX=0&sortspec=relevance&volume=14&firstpage=988&resourcetype=HWCIT">GeneWise</a> and <a rel="external" href="http://www.nature.com/ng/journal/v25/n2/abs/ng0600_235.html">Exofish</a> predictions with alignments of Tetraodon cDNAs to the genome. This was done automatically using <a rel="external" href="http://genome.cshlp.org/cgi/content/full/12/9/1418">GAZE</a> with a custom-designed configuration and gene structure model. Genoscope gene 1 {'label_key' => '[text_label] [display_label]','default' => {'MultiTop' => 'gene_label','contigviewbottom' => 'transcript_label','MultiBottom' => 'collapsed_label','contigviewtop' => 'gene_label','alignsliceviewbottom' => 'as_collapsed_label','cytoview' => 'gene_label'}, 'key' => 'ensembl', 'name' => 'Ensembl gene', 'multi_caption' => 'Ensembl genes, or Merged Ensembl and Havana genes'}
31 tRNAscan Prediction of tRNAs in genomic sequence is through <a rel="external" href="http://nar.oxfordjournals.org/cgi/content/full/25/5/955 ">tRNAscan-SE</a>. See <a href="/info/docs/genebuild/ncrna.html" class="cp=external">article.</a> tRNA 1
32 gene3d Gene3D analysis as of interpro_scan.pl gene3d 1 {'type'=>'alignment'}
33 ARRAY_UCR_GillMgMT_0.2K_v2 University of California, Riverside - Midgut and MT Chip reporters ARRAY_UCR_GillMgMT_0.2K_v2 1
34 GSC Ab initio prediction of protein coding genes by <a rel="external" href="http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6WK7-45VGF7T-9&_user=776054&_rdoc=1&_fmt=&_orig=search&_sort=d&view=c&_version=1&_urlVersion=0&_userid=776054&md5=aa15a5f8122912c172ddb9dd15b237dc">Genscan</a>, with parameters customised for accuracy in Tetraodon sequences GSC 1
35 guineapig_cdna Guineapig cDNAs from <a rel="external" href="http://www.ncbi.nlm.nih.gov/RefSeq/">NCBI RefSeq</a> and <a rel="external" href="http://www.ebi.ac.uk/embl/">EMBL</a> are aligned to the genome using <a rel="external" href="http://www.biomedcentral.com/1471-2105/6/31">Exonerate</a>. Guineapig cDNA 1 {'type' => 'cdna','default' => {'contigviewbottom' => 'stack'}}
36 snlRNA small nucleolar like RNA genes snlRNA 1 {'caption' => 'Non-coding','name' => 'Worm non-coding genes','label_key' => '[text_label] [display_label]','default' => {'contigviewbottom' => 'transcript_label','contigviewtop' => 'gene_label','cytoview' => 'gene_label','MultiTop' => 'gene_label','MultiBottom' => 'collapsed_label','alignsliceviewbottom' => 'as_collapsed_label'},'key' => 'ncRNA'}
37 platypus_protein Platypus proteins from <a rel="external" href="http://uniprot.org">UniProtKB</a> are aligned to the genome using <a rel="external" href="http://genome.cshlp.org/cgi/content/abstract/14/5/988?maxtoshow=&HITS=10&hits=10&RESULTFORMAT=&andorexactfulltext=and&searchid=1&FIRSTINDEX=0&sortspec=relevance&volume=14&firstpage=988&resourcetype=HWCIT">GeneWise</a>. Platypus prot. 1
38 GWS_UNI Alignment of a <a rel="external" href="http://www.uniprot.org/">Uniprot protein</a> to the genome by <a rel="external" href="http://genome.cshlp.org/cgi/content/abstract/14/5/988?maxtoshow=&HITS=10&hits=10&RESULTFORMAT=&andorexactfulltext=and&searchid=1&FIRSTINDEX=0&sortspec=relevance&volume=14&firstpage=988&resourcetype=HWCIT">GeneWise</a>. UniProt prot. 1
39 chimp_est Pan troglodytes 'Expressed Sequence Tags' (ESTs) from <a rel="external" href="http://www.ncbi.nlm.nih.gov/dbEST/">dbEST</a> aligned to the genome using <a rel="external" href="http://www.biomedcentral.com/1471-2105/6/31">Exonerate</a>. Chimpanzee EST 1 {'type' => 'est'}
40 FANTOM_CAGE These are short sequence tags from the start sites of polyA transcripts. These ditags were downloaded from the <a rel="external" href="http://fantom.gsc.riken.go.jp/">Riken Fantom</a> project and aligned to the genome using <a rel="external" href="http://www.biomedcentral.com/1471-2105/6/31">Exonerate</a>. Fantom CAGE tags 1
41 yeastX S. cerevisiae proteins aligned by WU-BlastX yeastX 1
42 cow_est Cow 'Expressed Sequence Tags' (ESTs) from <a rel="external" href="http://www.ncbi.nlm.nih.gov/dbEST/">dbEST</a> are aligned to the genome using <a rel="external" href="http://www.biomedcentral.com/1471-2105/6/31">Exonerate</a>. Cow EST 1 {'type'=>'est'}
43 opossum_cdna Opossum cDNAs are aligned to the genome using <a rel="external" href="http://www.biomedcentral.com/1471-2105/6/31">Exonerate</a>. Opossum cDNA 1 {'type' => 'cdna','default' => {'contigviewbottom' => 'stack'}}
44 sheep_bac_ends Sheep Bacterial Artificial Chromosome (end sequences) are aligned to the genome sequence using <a rel="external" href="http://www.biomedcentral.com/1471-2105/6/31">Exonerate</a>. Sheep BAC ends 1
45 orangutan_est Orangutan ESTs from EMBL aligned to the genome using Exonerate (G. Slater et al., BMC Bioinformatics. 2005 6:31) Orangutan EST 1 {'type'=>'est'}
46 Est2genome_other Alignment of non-human, non-mouse ESTs (expressed sequence tags) to the genome using the program <a rel="external" href="http://emboss.sourceforge.net/apps/cvs/emboss/apps/est2genome.html">Est2genome</a>. ESTs are from <a rel="external" href="http://www.ncbi.nlm.nih.gov/dbEST/">dbEST</a> Other EST (EST2genome) 1 {'type'=>'est'}
47 drosophila_protein FlyBase Drosophila proteins aligned to the genome using GeneWise (E.Birney et al., Genome Res. 2004 14:988-95) Drosophila prot. 1
48 ARRAY_LIV_GAMDETOX_0.25k_v2 Vectorbase probe alignments: LIV_GAMDETOX_0.25k_v2 OLIGO LIV_GAMDETOX_0.25k_v2 1
49 oxford_FGU Gene predictions generated by <a rel="external" href="http://www.mrcfgu.ox.ac.uk/research/chris-p-ponting/">Chris Ponting's group</a> at the <a rel="external" href="http://www.mrcfgu.ox.ac.uk/">MRC-FGU, Oxford</a>. FGU gene 1 {'label_key' => '[text_label] [display_label]','default' => {'contigviewbottom' => 'transcript_label','contigviewtop' => 'gene_label','cytoview' => 'gene_label','MultiTop' => 'gene_label','MultiBottom' => 'collapsed_label','alignsliceviewbottom' => 'as_collapsed_label'}}
50 hmmpanther HMM-Panther families hmmpanther 1 {'type'=>'alignment'}
51 est_bestn_3prim 3' 'Expressed Sequence Tags' (ESTs) are mapped on the genome using <a rel="external" href="http://www.biomedcentral.com/1471-2105/6/31">Exonerate</a>, and the best hit is shown. best hit 3' EST 1 {'type'=>'est'}
52 wormbase This gene was annotated and aligned to the genome by <a rel="external" href="http://www.wormbase.org">Wormbase</a> through a process of automatic and manual curation. Worm gene 1 {'caption' => 'Genes (Worm)','name' => 'Wormbase','label_key' => '[text_label] [display_label]','default' => {'contigviewbottom' => 'transcript_label','contigviewtop' => 'gene_label','cytoview' => 'gene_label','MultiTop' => 'gene_label','MultiBottom' => 'collapsed_label','alignsliceviewbottom' => 'as_collapsed_label'},'key' => 'wormbase'}
53 kyotograil_2004 C. intestinalis gene models from the <a rel="external" href="http://ghost.zool.kyoto-u.ac.jp/indexr1.html">KYOTOGRAIL set, version 2004,</a> aligned to the genome using <a rel="external" href="http://www.biomedcentral.com/1471-2105/6/31">Exonerate</a>. Kyotograil 04 prediction 1 {'type'=>'est'}
54 ARRAY_EMBL_MMC2_12k_v1 Vectorbase probe alignments: EMBL_MMC2_12k_v1 OLIGO EMBL_MMC2_12k_v1 1
55 EG3_Fr Evolutionary conserved regions ("Ecores") are inferred from alignments of the Fugu and Tetraodon genomes by <a rel="external" href="http://www.nature.com/ng/journal/v25/n2/abs/ng0600_235.html">Exofish, H. Roest Crollius et al.,</a> and grouped into contiguous, consistent sets ("Ecotigs") Takifugu Ecores 1 {'default' => {'contigviewbottom' => 'stack'}}
#56 other_proteins For various species, proteins from <a rel="external" href="http://uniprot.org">UniProtKB</a> are aligned to the genome with <a rel="external" href="http://genome.cshlp.org/cgi/content/abstract/14/5/988?maxtoshow=&HITS=10&hits=10&RESULTFORMAT=&andorexactfulltext=and&searchid=1&FIRSTINDEX=0&sortspec=relevance&volume=14&firstpage=988&resourcetype=HWCIT">GeneWise</a>. Other sp. prot. 1
#57 Stick_ab_initio_RepeatMask Interspersed repeats and low complexity sequence identified by <a rel="external" href="http://www.repeatmasker.org">RepeatMasker</a> using ab initio repeat profiles specific to Gasterosteus aculeatus. Repeats (Recon) 1
58 RNAi Aligned probes from RNA interference experiments. RNAi 1
59 anopheles_cdna_est Anopheles ESTs and cDNAs aligned to the genome using Exonerate (G. Slater et al., BMC Bioinformatics. 2005 6:31) RNA (best) 1 {'type' => 'est','default' => {'contigviewbottom' => 'stack'}}
60 celegans_est Caenorhabditis elegans 'Expressed Sequence Tags' (ESTs) from <a rel="external" href="http://www.ncbi.nlm.nih.gov/dbEST/">dbEST</a> are aligned to the genome using <a rel="external" href="http://www.biomedcentral.com/1471-2105/6/31">Exonerate</a>. C.elegans EST 1 {'type' => 'est','default' => {'contigviewbottom' => 'stack'}}
61 horse_est Horse 'Expressed Sequence Tags' (ESTs) from <a rel="external" href="http://www.ncbi.nlm.nih.gov/dbEST/">dbEST</a> are aligned to the genome using <a rel="external" href="http://www.biomedcentral.com/1471-2105/6/31">Exonerate</a>. Horse EST 1 {'type'=>'est' }
62 est_bestn_5prim 5' 'Expressed Sequence Tags' (ESTs) are mapped on the genome using <a rel="external" href="http://www.biomedcentral.com/1471-2105/6/31">Exonerate</a>, and the best hit is shown. best hit 5' EST 1 {'type'=>'est'}
63 yeastP S. cerevisiae proteins aligned by WU-BlastP yeastP 1 {'type'=>'alignment'}
64 EG3_Rn Evolutionary conserved regions ("Ecores") are inferred from alignments of the Rat and Tetraodon genomes by <a rel="external" href="http://www.nature.com/ng/journal/v25/n2/abs/ng0600_235.html">Exofish, H. Roest Crollius et al.,</a> and grouped into contiguous, consistent sets ("Ecotigs") Rat Ecores 1 {'default' => {'contigviewbottom' => 'stack'}}
65 cow_cdna Cow cDNAs from <a rel="external" href="http://www.ncbi.nlm.nih.gov/RefSeq/">NCBI RefSeq</a> and <a rel="external" href="http://www.ebi.ac.uk/embl/">EMBL</a> are aligned to the genome using <a rel="external" href="http://www.biomedcentral.com/1471-2105/6/31">Exonerate</a>. Cow cDNA 1 {'default' => {'contigviewbottom' => 'stack'},'type' => 'cdna'}
66 RepeatMasker_RECON Interspersed repeats identified by RepeatMasker (http://www.repeatmasker.org/) RepeatMask 1
67 est_embl 'Expressed Sequence Tags' (ESTs) from the <a rel="external" href="http://www.ebi.ac.uk/embl/">EMBL</a> database are aligned to the genome using <a rel="external" href="http://www.biomedcentral.com/1471-2105/6/31">Exonerate</a>. EMBL EST 1 {'type' => 'est'};68 chicken_protein Chicken protein sequences from <a rel="external" href="http://uniprot.org">UniProtKB</a> and <a rel="external" href="http://www.ncbi.nlm.nih.gov/RefSeq/">NCBI RefSeq</a> are aligned to the genome using <a rel="external" href="http://genome.cshlp.org/cgi/content/abstract/14/5/988?maxtoshow=&HITS=10&hits=10&RESULTFORMAT=&andorexactfulltext=and&searchid=1&FIRSTINDEX=0&sortspec=relevance&volume=14&firstpage=988&resourcetype=HWCIT">GeneWise</a>. Chicken prot. 1
69 dog_protein Dog proteins from <a rel="external" href="http://uniprot.org">UniProtKB</a> are aligned to the genome using <a rel="external" href="http://genome.cshlp.org/cgi/content/abstract/14/5/988?maxtoshow=&HITS=10&hits=10&RESULTFORMAT=&andorexactfulltext=and&searchid=1&FIRSTINDEX=0&sortspec=relevance&volume=14&firstpage=988&resourcetype=HWCIT">GeneWise</a>. Dog protein 1
70 chimp_human_protein Human protein sequence aligned to the chimp genome by projection or by using <a rel="external" href="http://www.biomedcentral.com/1471-2105/6/31">Exonerate</a>. human prot. 1
71 human_est Homo sapiens 'Expressed Sequence Tags' (ESTs) from <a rel="external" href="http://www.ncbi.nlm.nih.gov/dbEST/">dbEST</a> are aligned to the genome using <a rel="external" href="http://www.biomedcentral.com/1471-2105/6/31">Exonerate</a>. Human EST 1 {'type'=>'est'}
72 cow_protein Cow protein sequences from <a rel="external" href="http://uniprot.org">UniProtKB</a> and <a rel="external" href="http://www.ncbi.nlm.nih.gov/RefSeq/">NCBI RefSeq</a> are aligned to the genome using <a rel="external" href="http://genome.cshlp.org/cgi/content/abstract/14/5/988?maxtoshow=&HITS=10&hits=10&RESULTFORMAT=&andorexactfulltext=and&searchid=1&FIRSTINDEX=0&sortspec=relevance&volume=14&firstpage=988&resourcetype=HWCIT">GeneWise</a>. Cow prot. 1
73 caenorhabditis_est Caenorhabditis ESTs aligned to the genome using BLAT (excluding C.elegans) caenorhabditis EST 1 {'type'=>'est'}
74 singapore_est Expressed Sequence Tag (EST)-based gene prediction provided by B. Kumarasamy and E. Stupka. Singapore gene 1 {'label_key' => '[text_label] [display_label]','key' => 'singapore_est','dna_align_feature' => {'do_not_display' => 1}}
75 Uniprot_SW Proteins from the <a rel="external" href="http://uniprot.org">UniProtKB Swiss-Prot</a> database, aligned to the genome. UniProt prot. 1
76 drosophila_est Drosophila melanogaster 'Expressed Sequence Tags' (ESTs) from <a rel="external" href="http://www.ncbi.nlm.nih.gov/dbEST/">dbEST</a> are aligned to the genome using <a rel="external" href="http://www.biomedcentral.com/1471-2105/6/31">Exonerate</a>. Fly EST 1 {'type'=>'est'}
77 Uniprot_non_mammal Non-mammal proteins from the <a rel="external" href="http://uniprot.org">UniProtKB</a> database, positioned on the genome through BLASTP of Genscan-predicted (non-mammalian) peptides to UniProtKB proteins. non-mammal UniProt prot. 1
78 drosophila_cdna_all Drosophila melanogaster cDNA sequences from <a rel="external" href="http://www.fruitfly.org">BDGP</a> are aligned to the genome using <a rel="external" href="http://www.biomedcentral.com/1471-2105/6/31">Exonerate</a>. Fly cDNA 1 {'default' => {'contigviewbottom' => 'stack'},'type' => 'cdna'}
79 GID Ab initio prediction of protein coding genes by <a rel="external" href="http://www1.imim.es/software/geneid/">Geneid</a>, with parameters customised for accuracy in Tetraodon sequences. Geneid prediction 1
80 slimswissprotP Swissprot proteins aligned by WU-BlastP slimswissprotP 1 {'type'=>'alignment'}
81 ensembl_havana_gene Gene containing both Ensembl genebuild transcripts and <a rel="external" href="http://vega.sanger.ac.uk/index.html">Havana</a> manual curation, see <a href="/info/docs/genebuild/genome_annotation.html" class="cp-external">article</a>. Ensembl/Havana merge gene 1 {'colour_key' => '[biotype]_[status]','caption' => 'Ensembl/Havana gene','name' => 'Merged Ensembl and Havana Genes','label_key' => '[text_label] [display_label]','default' => {'contigviewbottom' => 'transcript_label','contigviewtop' => 'gene_label','cytoview' => 'gene_label','MultiTop' => 'gene_label','MultiBottom' => 'collapsed_label','alignsliceviewbottom' => 'as_collapsed_label'},'key' => 'ensembl','multi_caption' => 'Ensembl genes, or Merged Ensembl and Havana genes'}
82 ncoils Prediction of coiled-coil regions in proteins is by <a rel="external" href="http://www.sciencemag.org/cgi/reprint/252/5009/1162">Ncoils</a>. Coiled-coils (Ncoils) 1
83 havana Manually annotated transcripts (determined on a case-by-case basis) from the <a rel="external" href="http://www.sanger.ac.uk/HGP/havana/havana.shtml">Havana</a> project. Havana gene 1 {'colour_key' => '[biotype]_[status]','caption' => 'Ensembl/Havana gene','name' => 'Merged Ensembl and Havana Genes','label_key' => '[text_label] [display_label]','default' => {'contigviewbottom' => 'transcript_label','contigviewtop' => 'gene_label','cytoview' => 'gene_label','MultiTop' => 'gene_label','MultiBottom' => 'collapsed_label','alignsliceviewbottom' => 'as_collapsed_label'},'key' => 'ensembl','multi_caption' => 'Ensembl genes, or Merged Ensembl and Havana genes'}
84 Pfam Protein domains and motifs in the <a rel="external" href="http://nar.oxfordjournals.org/cgi/content/abstract/32/suppl_1/D138?maxtoshow=&HITS=10&hits=10&RESULTFORMAT=1&author1=Bateman&andorexacttitle=and&andorexacttitleabs=and&andorexactfulltext=and&searchid=1&FIRSTINDEX=0&sortspec=relevance&resourcetype=HWCIT">Pfam</a> database. Pfam domain 1 {'type'=>'domain'}
85 PercentGC Percentage of G/C bases in the sequence. GC content 1
86 knownGeneDensity Known gene density as calculated by <a rel="external" href="http://cvs.sanger.ac.uk/cgi-bin/viewvc.cgi/ensembl/misc-scripts/density_feature/gene_density_calc.pl?root=ensembl&view=markup">gene_density_calc.pl</a>. Genes (density) 1
87 chimp_protein Pan troglodyes protein sequences from <a rel="external" href="http://uniprot.org">UniProtKB</a> and <a rel="external" href="http://www.ncbi.nlm.nih.gov/RefSeq/">NCBI RefSeq</a> are aligned to the genome using <a rel="external" href="http://genome.cshlp.org/cgi/content/abstract/14/5/988?maxtoshow=&HITS=10&hits=10&RESULTFORMAT=&andorexactfulltext=and&searchid=1&FIRSTINDEX=0&sortspec=relevance&volume=14&firstpage=988&resourcetype=HWCIT">GeneWise</a>. Chimpanzee prot. 1
88 jgi_v2 Alignments to Ciona intestinalis gene models predicted by JGI on assembly version 2.0 ( http://genome.jgi-psf.org/Cioin2/Cioin2.home.html ) JGI v2 prediction 1
89 macaque_cdna Macaque cDNAs from <a rel="external" href="http://www.ncbi.nlm.nih.gov/RefSeq/">NCBI RefSeq</a> and <a rel="external" href="http://www.ebi.ac.uk/embl/">EMBL</a> are aligned to the genome using <a rel="external" href="http://www.biomedcentral.com/1471-2105/6/31">Exonerate</a>. Macaque cDNA 1 {'default' => {'contigviewbottom' => 'stack'},'type' => 'cdna'}
90 snRNA small nuclear RNA genes snRNA 1 {'caption' => 'Non-coding','name' => 'Worm non-coding genes','label_key' => '[text_label] [display_label]','default' => {'contigviewbottom' => 'transcript_label','contigviewtop' => 'gene_label','cytoview' => 'gene_label','MultiTop' => 'gene_label','MultiBottom' => 'collapsed_label','alignsliceviewbottom' => 'as_collapsed_label'},'key' => 'ncRNA'}
91 ARRAY_ND_TIGRTC_9.6K_v1 University of Notre Dame - TIGRTC array reporters ARRAY_ND_TIGRTC_9.6K_v1 1
92 GadflyP FlyBase proteins aligned by WU-BlastP GadflyP 1 {'type'=>'alignment'}
93 rRNA ribosomal RNA genes rRNA 1 {'caption' => 'Non-coding','name' => 'Worm non-coding genes','label_key' => '[text_label] [display_label]','default' => {'contigviewbottom' => 'transcript_label','contigviewtop' => 'gene_label','cytoview' => 'gene_label','MultiTop' => 'gene_label','MultiBottom' => 'collapsed_label','alignsliceviewbottom' => 'as_collapsed_label'},'key' => 'ncRNA'}
94 tetraodon_protein Tetraodon proteins from <a rel="external" href="http://uniprot.org">UniProtKB</a> are aligned to the genome using <a rel="external" href="http://genome.cshlp.org/cgi/content/abstract/14/5/988?maxtoshow=&HITS=10&hits=10&RESULTFORMAT=&andorexactfulltext=and&searchid=1&FIRSTINDEX=0&sortspec=relevance&volume=14&firstpage=988&resourcetype=HWCIT">GeneWise</a>. Tetraodon prot. 1
95 cDNA_update The latest set of cDNAs for this species from EMBL-nucleotides and NCBI RefSeq were aligned to the current genome using <a rel="external" href="http://www.ebi.ac.uk/~guy/exonerate/">Exonerate</a>. cDNA update 1 {'gene' => {'do_not_display' => 1},'label_key' => '[text_label] [display_label]','default' => {'contigviewbottom' => 'stack'},'type' => 'cdna'}
96 cint_est Ciona intestinalis 'Expressed Sequence Tags' (ESTs) from <a rel="external" href="http://www.ncbi.nlm.nih.gov/dbEST/">dbEST</a> and the <a rel="external" href="http://ghost.zool.kyoto-u.ac.jp/indexr1.html">Ghost Database</a> are aligned to the genome using <a rel="external" href="http://www.biomedcentral.com/1471-2105/6/31">Exonerate</a>. C.intestinalis EST 1 {'type'=>'est'}
97 savignyi_est Ciona savignyi 'Expressed Sequence Tags' (ESTs) were aligned to corrected cDNA sequences from the <a rel="external" href="http://ghost.zool.kyoto-u.ac.jp/indexr1.html">Kyoto-EST-set</a> using <a rel="external" href="http://www.biomedcentral.com/1471-2105/6/31">Exonerate</a>. C.savignyi EST 1 {'type'=>'est'}
98 UniprotBlast WuBLASTX of genomic segments against UniprotKB protein set UniProtKB BLAST 1
99 blastprodom NCBI-BlastP search against ProDom families blastprodom 1 {'type'=>'alignment'}
100 zfish_EST Danio rerio 'Expressed Sequence Tags' (ESTs) from <a rel="external" href="http://www.ncbi.nlm.nih.gov/dbEST/">dbEST</a> are aligned to the genome using <a rel="external" href="http://www.biomedcentral.com/1471-2105/6/31">Exonerate</a>. Zebrafish EST 1 {'type'=>'est'}
101 TRF <a rel="external" href="http://nar.oxfordjournals.org/cgi/content/full/27/2/573?maxtoshow=&HITS=10&hits=10&RESULTFORMAT=1&author1=Benson&andorexacttitle=and&andorexacttitleabs=and&andorexactfulltext=and&searchid=1&FIRSTINDEX=0&sortspec=relevance&fdate=1/1/1999&tdate=12/31/1999&resourcetype=HWCIT">Tandem Repeats Finder</a> locates adjacent copies of a pattern of nucleotides. Tandem repeats (TRF) 1
102 Marker Markers, or sequence tagged sites (STS), from <a rel="external" href="http://www.ncbi.nlm.nih.gov/sites/entrez?db=unists">UniSTS</a> are aligned to the genome using <a rel="external" href="http://genome.cshlp.org/cgi/content/full/7/5/541">Electronic PCR (e-PCR)</a>. Marker 1
103 transposable_element Feature imported from <a rel="external" href="http://www.flybase.org">FlyBase</a>. TE 1
104 fugu_cDNA Takifugu cDNAs from <a rel="external" href="http://www.ebi.ac.uk/embl/">EMBL</a> and <a rel="external" href="http://www.ncbi.nlm.nih.gov/Genbank/">Genbank</a> are aligned to the genome using <a rel="external" href="http://www.biomedcentral.com/1471-2105/6/31">Exonerate</a>. Takifugu cDNA 1 {'default' => {'contigviewbottom' => 'stack'},'type' => 'cdna'}
105 ensembl_segment Immunoglubulin (Ig) and T-cell receptor (TcR) genes are imported from the <a rel="external" href="http://imgt.cines.fr">IMGT database</a> and aligned to the genome using <a rel="external" href="http://www.biomedcentral.com/1471-2105/6/31">Exonerate</a>. See <a href="/info/docs/genebuild/ig_tcr.html" class="cp-external">article</a>. Ig/T-cell receptor gene 1 {'colour_key' => '[biotype]_[status]','caption' => 'Ensembl/Havana gene','name' => 'Merged Ensembl and Havana Genes','label_key' => '[text_label] [display_label]','default' => {'contigviewbottom' => 'transcript_label','contigviewtop' => 'gene_label','cytoview' => 'gene_label','MultiTop' => 'gene_label','MultiBottom' => 'collapsed_label','alignsliceviewbottom' => 'as_collapsed_label'},'key' => 'ensembl','multi_caption' => 'Ensembl genes, or Merged Ensembl and Havana genes'}
106 chimp_cdna Pan troglodytes cDNAs from <a rel="external" href="http://www.ncbi.nlm.nih.gov/RefSeq/">NCBI RefSeq</a> and <a rel="external" href="http://www.ebi.ac.uk/embl/">EMBL</a> are aligned to the genome using <a rel="external" href="http://www.biomedcentral.com/1471-2105/6/31">Exonerate</a>. Chimpanzee cDNA 1 {'default' => {'contigviewbottom' => 'stack'},'type' => 'cdna'}
107 qtl Quantitative Trait Loci (QTL) features. QTL 1
108 Tmhmm Prediction of transmembrane helices in proteins by <a rel="external" href="http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6WK7-457D7V9-K&_user=776054&_rdoc=1&_fmt=&_orig=search&_sort=d&view=c&_version=1&_urlVersion=0&_userid=776054&md5=a113464457fa5206c6699b9d464cbfee">TMHMM</a>. Transmembrane helices 1
109 rat_cdna Rattus norvegicus cDNAs from <a rel="external" href="http://www.ncbi.nlm.nih.gov/RefSeq/">NCBI RefSeq</a> and <a rel="external" href="http://www.ebi.ac.uk/embl/">EMBL</a> are aligned to the genome using <a rel="external" href="http://www.biomedcentral.com/1471-2105/6/31">Exonerate</a>. Rat RefSeq/EMBL cDNA 1 {'dna_align_feature' => {'do_not_display' => '1'},'default' => {'contigviewbottom' => 'stack'},'type' => 'cdna'}
110 sequence_variant Feature imported from <a rel="external" href="http://www.flybase.org">FlyBase</a>. Sequence Variant 1
111 CCDS Protein coding sequences agreed upon by the Consensus Coding Sequence project, or <a href="/info/docs/genebuild/ccds.html" class="cp-external">CCDS</a>. CCDS set 1 {'default' => {'contigviewbottom' => 'normal'},'type' => 'cdna'}
112 platypus_olfactory_receptors Manually curated olfactory receptor sequences from <a rel="external" href="http://www.funpecrp.com.br/gmr2008b/issue.asp?volume=541&capitulo=551#anc_206">Tsviya Olender</a> P.O.R. gene 1 {'label_key' => '[text_label] [display_label]','default' => {'contigviewbottom' => 'transcript_label','contigviewtop' => 'gene_label','cytoview' => 'gene_label','MultiTop' => 'gene_label','MultiBottom' => 'collapsed_label','alignsliceviewbottom' => 'as_collapsed_label'}}
113 MetazoaBlast Proteins placed on the genome with BLASTX Metazoa BLAST 1
114 Ncoils Prediction of coiled-coil regions in proteins is by <a rel="external" href="http://www.sciencemag.org/cgi/reprint/252/5009/1162">Ncoils</a>. Coiled-coils (Ncoils) 1
115 Arma_ab_initio_RepeatMask Interspersed repeats and low complexity sequence identified by <a rel="external" href="http://www.repeatmasker.org/">RepeatMasker</a> using ab initio repeat profiles specific to Dasypus novemcinctus. Repeats (Recon) 1
116 human_ensembl_proteins Selected Ensembl-predicted human peptide sequences aligned to the genome using the whole genome alignment to gene (WGA2Gene) projection method or <a rel="external" href="http://www.biomedcentral.com/1471-2105/6/31">Exonerate</a>. Human Ensembl prot. 1 {'label_key' => '[text_label] [display_label]','default' => {'contigviewbottom' => 'transcript_label','contigviewtop' => 'gene_label','cytoview' => 'gene_label','MultiTop' => 'gene_label','MultiBottom' => 'collapsed_label','alignsliceviewbottom' => 'as_collapsed_label'}}
117 macaque_refseq Macaque proteins from <a rel="external" href="http://www.ncbi.nlm.nih.gov/RefSeq/">NCBI RefSeq</a> used in the <a href="/info/docs/genebuild/index.html" class="cp-external">genebuild</a> are aligned to the genome using <a rel="external" href="http://genome.cshlp.org/cgi/content/abstract/14/5/988?maxtoshow=&HITS=10&hits=10&RESULTFORMAT=&andorexactfulltext=and&searchid=1&FIRSTINDEX=0&sortspec=relevance&volume=14&firstpage=988&resourcetype=HWCIT">GeneWise</a>. Macaque RefSeq prot. 1
118 macaque_est Macaque 'Expressed Sequence Tags' (ESTs) from <a rel="external" href="http://www.ncbi.nlm.nih.gov/dbEST/">dbEST</a> are aligned to the genome using <a rel="external" href="http://www.biomedcentral.com/1471-2105/6/31">Exonerate</a>. Macaque EST 1 {'type'=>'est'}
119 macaque_protein Macaque proteins from <a rel="external" href="http://uniprot.org">UniProtKB</a> are aligned to the genome using <a rel="external" href="http://genome.cshlp.org/cgi/content/abstract/14/5/988?maxtoshow=&HITS=10&hits=10&RESULTFORMAT=&andorexactfulltext=and&searchid=1&FIRSTINDEX=0&sortspec=relevance&volume=14&firstpage=988&resourcetype=HWCIT">GeneWise</a>. Macaque UniProt prot. 1
120 ncRNA Non-coding RNA (ncRNA) is predicted using sequences from <a href="http://rfam.sanger.ac.uk">RFAM</a> and <a href="http://microrna.sanger.ac.uk/sequences/index.shtml">miRBase</a>. See <a href="/info/docs/genebuild/ncrna.html" class="cp-external">article</a>. ncRNA gene 1 {'colour_key' => 'rna_[status]','label_key' => '[text_label] [display_label]','default' => {'contigviewbottom' => 'transcript_label','contigviewtop' => 'gene_label','cytoview' => 'gene_label','MultiTop' => 'gene_label','MultiBottom' => 'collapsed_label','alignsliceviewbottom' => 'as_collapsed_label'}}
121 xlaevis_EST Xenopus laevis 'Expressed Sequence Tags' (ESTs) from <a rel="external" href="http://www.ncbi.nlm.nih.gov/dbEST/">dbEST</a> are aligned to the genome using <a rel="external" href="http://www.biomedcentral.com/1471-2105/6/31">Exonerate</a>. X.laevis EST 1 {'type'=>'est'}
122 snpDensity Density of Single Nucleotide Polymorphisms (SNPs) calculated by variation_density.pl (see scripts at the <a rel="external" href="http://cvs.sanger.ac.uk/cgi-bin/viewvc.cgi/?root=ensembl">Sanger Institute CVS</a> repository). SNP Density 1
123 Medaka_TranscriptCoalescer Medaka genes, predicted using Medaka ESTs as input for the gene-predicting module TranscriptCoalescer. EST-based gene 1 {'label_key' => '[text_label] [display_label]','key' => 'estgene','label' => '[text_label] [display_label]','name' => 'EST-based gene'}
124 human_refseq Human proteins from <a rel="external" href="http://www.ncbi.nlm.nih.gov/RefSeq/">NCBI RefSeq</a> used in the <a href="/info/docs/genebuild/index.html" class="cp-external">genebuild</a> are aligned to the genome using <a rel="external" href="http://genome.cshlp.org/cgi/content/abstract/14/5/988?maxtoshow=&HITS=10&hits=10&RESULTFORMAT=&andorexactfulltext=and&searchid=1&FIRSTINDEX=0&sortspec=relevance&volume=14&firstpage=988&resourcetype=HWCIT">GeneWise</a>. Human RefSeq prot. 1
125 Vertrna Positions of vertebrate mRNAs along the genome. mRNAs are from the <a rel="external" href="http://www.ebi.ac.uk/embl/">EMBL</a> database. Initial alignments are performed using TBLASTN of Genscan-predicted peptides against EMBL mRNAs. EMBL vertebrate cDNA 1 {'type' => 'cdna','default' => {'contigviewbottom'=>'stack'}}
126 fugu_cdna Takifugu cDNAs from <a rel="external" href="http://www.ebi.ac.uk/embl/">EMBL</a> and <a rel="external" href="http://www.ncbi.nlm.nih.gov/Genbank/">Genbank</a> are aligned to the genome using <a rel="external" href="http://www.biomedcentral.com/1471-2105/6/31">Exonerate</a>. Takifugu cDNA 1 {'default' => {'contigviewbottom' => 'stack'},'type' => 'cdna'}
#127 Tenrec_ab_initio_RepeatMask Interspersed repeats and low complexity sequence identified by <a rel="external" href="http://www.repeatmasker.org">RepeatMasker</a> using ab initio repeat profiles specific to Echinops telfairi. Repeats (Recon) 1
128 Uniprot Proteins from the <a rel="external" href="http://uniprot.org">UniProtKB</a> database, positioned on the genome through BLASTP of Genscan-predicted peptides to UniProtKB proteins. UniProtKB prot. 1
129 Tigrfam Protein domains and motifs in the <a rel="external" href="http://nar.oxfordjournals.org/cgi/content/full/31/1/371?maxtoshow=&HITS=10&hits=10&RESULTFORMAT=1&author1=Haft&andorexacttitle=and&andorexacttitleabs=and&andorexactfulltext=and&searchid=1&FIRSTINDEX=0&sortspec=relevance&fdate=1/1/2003&tdate=12/31/2003&resourcetype=HWCIT">TIGRFAM</a> database. TIGRFAM domain 1 {'type'=>'domain'}
130 fgenesh Ab initio prediction of protein coding genes, based on the genomic sequence alone <a rel="external" href="http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=10779491">AA Salamov et al., Genome Res. 2000 4:516-22</a>. FGENESH prediction 1
131 scanprosite Protein domains and motifs from the <a rel="external" href="http://www.ebi.ac.uk/ppsearch/">PROSITE</a> profiles database are aligned to the genome. PROSITE patterns 1 {'type'=>'domain'}
132 stickleback_protein Gasterosteus aculeatus proteins from <a rel="external" href="http://uniprot.org">UniProtKB</a> are aligned to the genome using <a rel="external" href="http://genome.cshlp.org/cgi/content/abstract/14/5/988?maxtoshow=&HITS=10&hits=10&RESULTFORMAT=&andorexactfulltext=and&searchid=1&FIRSTINDEX=0&sortspec=relevance&volume=14&firstpage=988&resourcetype=HWCIT">GeneWise</a>. Stickleback prot. 1
133 Medaka_Genome_Project Genes predicted by the Medaka Genome Project, viz. the University of Tokyo (http://medaka.utgenome.org/) and the National Institute of Genetics (http:// dolphin.lab.nig.ac.jp/medaka/). MGP gene 1 {'label_key' => '[text_label] [display_label]','label' => '[text_label] [display_label]'}
134 otter Finished genomic sequence is analysed on a clone by clone basis using a combination of similarity searches against DNA and protein databases as well as a series of ab initio gene predictions (GENSCAN, Augustus). In addition, comparative analysis using vertebrate datasets is used to aid novel gene discovery. The data gathered in these steps is then used to manually annotate the clone adding gene structures, descriptions and poly-A features. The annotation is based on supporting evidence only. Vega Havana gene 1 {'colour_key'=>'[gene.logic_name]_[gene.biotype]'}
#135 est_genebuilder ESTs are mapped on the genome using <a rel="external" href="http://www.biomedcentral.com/1471-2105/6/31">Exonerate</a>. The Cluster-Merge algorithm <a rel="external" href="http://genome.cshlp.org/cgi/content/full/14/5/976">(E.Eyras et al.)</a> is used to infer a set of gene structures (including isoforms) from the alignments. EST-based gene 1
136 medaka_5pSAGE Medaka 5pSAGE data provided by the University of Tokyo and aligned to the genome using Exonerate (G. Slater et al., BMC Bioinformatics. 2005 6:31) Medaka 5' SAGE 1
137 EG3_Gg Evolutionary conserved regions("Ecores") are inferred from alignments of the Chicken and Tetraodon genomes by <a rel="external" href="http://www.nature.com/ng/journal/v25/n2/abs/ng0600_235.html">Exofish, H. Roest Crollius et al.,</a> and grouped into contiguous, consistent sets ("Ecotigs") Chicken Ecores 1 {'default' => {'contigviewbottom' => 'stack'}}138 RfamBlast <a href="/info/docs/genebuild/ncrna.html" class="cp-external">Positions</a>Positions of ncRNAs (non-coding RNAs) from the <a rel="external" href="http://rfam.sanger.ac.uk/">Rfam </a> database are shown. Initial BLASTN hits of genomic sequence to RFAM ncRNAs are clustered and filtered by E value. These hits are supporting evidence for ncRNA genes. RFAM ncRNA gene 1 {'type'=>'rna'}
139 orangutan_protein Orangutan proteins from Swiss-Prot/TrEMBL aligned to the genome using GeneWise (E. Birney et al., Genome Res. 2004 14:988-95) Orangutan prot. 1
140 fugu_est Takifugu 'Expressed Sequence Tags' (ESTs) from <a rel="external" href="http://www.ncbi.nlm.nih.gov/dbEST/">dbEST</a> are aligned to the genome using <a rel="external" href="http://www.biomedcentral.com/1471-2105/6/31">Exonerate</a>. Takifugu EST 1 {'type'=>'est'}
141 EukaryotaBlast Proteins placed on the genome with BLASTX Eukaryota BLAST 1
142 aedes_protein VB EST-supported Aedes proteins aligned to the genome using GeneWise (E.Birney et al., Genome Res. 2004 14:988-95) Aedes prot. 1
143 snoRNA small nucleolar RNA genes snoRNA 1 {'caption' => 'Non-coding','name' => 'Worm non-coding genes','label_key' => '[text_label] [display_label]','default' => {'contigviewbottom' => 'transcript_label','contigviewtop' => 'gene_label','cytoview' => 'gene_label','MultiTop' => 'gene_label','MultiBottom' => 'collapsed_label','alignsliceviewbottom' => 'as_collapsed_label'},'key' => 'ncRNA'}
144 other_est For various species, 'Expressed Sequence Tags' (ESTs) from <a rel="external" href="http://www.ncbi.nlm.nih.gov/dbEST/">dbEST</a> are aligned to the genome using <a rel="external" href="http://www.biomedcentral.com/1471-2105/6/31">Exonerate</a>. Various EST 1 {'type'=>'est'}
145 geneDensity Known gene density as calculated by <a rel="external" href="http://cvs.sanger.ac.uk/cgi-bin/viewvc.cgi/ensembl/misc-scripts/density_feature/gene_density_calc.pl?root=ensembl&view=markup">gene_density_calc.pl</a>. Genes (density) 1
146 oligo Feature imported from <a rel="external" href="http://www.flybase.org">FlyBase</a>. Oligo 1
147 otter_external See <a href="http://vega.sanger.ac.uk/info/about/man_annotation.html" target="external">the Vega website</a> for details of the approaches used for the annotation of external Vega genes Vega External gene 1 {'colour_key'=>'[gene.logic_name]_[gene.biotype]'}
148 PIRSF Protein domains and motifs from the <a rel="external" href="http://pir.georgetown.edu/pirwww/index.shtml">PIR (Protein Information Resource)</a> Superfamily database. PIRSF domain 1 {'type'=>'domain'}
149 Uniprot_non_vertebrate Non-vertebrate proteins from the <a rel="external" href="http://uniprot.org">UniProtKB</a> database, positioned on the genome through BLASTP of Genscan-predicted (non-mammalian) peptides to UniProtKB proteins. non-vertebrate UniProt prot. 1
150 medaka_cdna Medaka cDNAs from <a rel="external" href="http://www.ncbi.nlm.nih.gov/RefSeq/">NCBI RefSeq</a> and <a rel="external" href="http://www.ebi.ac.uk/embl/">EMBL</a> are aligned to the genome aligned to the genome using <a rel="external" href="http://www.ebi.ac.uk/~guy/exonerate/">Exonerate</a>. Medaka RefSeq/EMBL cDNA 1 {'default' => {'contigviewbottom' => 'stack'},'type' => 'cdna'}
151 mouse_est Murine 'Expressed Sequence Tags' (ESTs) from <a rel="external" href="http://www.ncbi.nlm.nih.gov/dbEST/">dbEST</a> are aligned to the genome using <a rel="external" href="http://www.biomedcentral.com/1471-2105/6/31">Exonerate</a>. Mouse EST 1 {'type'=>'est'}
152 xtrop_protein Xenopus tropicalis proteins from <a rel="external" href="http://uniprot.org">UniProtKB</a> and <a rel="external" href="http://www.ncbi.nlm.nih.gov/RefSeq/">NCBI RefSeq</a> are aligned to the genome using <a rel="external" href="http://genome.cshlp.org/cgi/content/abstract/14/5/988?maxtoshow=&HITS=10&hits=10&RESULTFORMAT=&andorexactfulltext=and&searchid=1&FIRSTINDEX=0&sortspec=relevance&volume=14&firstpage=988&resourcetype=HWCIT">GeneWise</a>. X.tropicalis prot. 1
153 chicken_cDNA Chicken cDNAs from <a rel="external" href="http://www.ncbi.nlm.nih.gov/RefSeq/">NCBI RefSeq</a> and <a rel="external" href="http://www.ebi.ac.uk/embl/">EMBL</a> are aligned to the genome using <a rel="external" href="http://www.biomedcentral.com/1471-2105/6/31">Exonerate</a>. Chicken cDNA 1 {'default' => {'contigviewbottom' => 'stack'},'type' => 'cdna'}
154 wormpepX C. elegans proteins aligned by WU-BlastX wormpepX 1
155 pfscan Protein domains and motifs from the <a rel="external" href="http://www.ebi.ac.uk/ppsearch/">PROSITE</a> profiles database are aligned to the genome. PROSITE profiles 1 {'type'=>'domain'}
156 mouse_protein Murine proteins from <a rel="external" href="http://uniprot.org">UniProtKB</a> are aligned to the genome using <a rel="external" href="http://genome.cshlp.org/cgi/content/abstract/14/5/988?maxtoshow=&HITS=10&hits=10&RESULTFORMAT=&andorexactfulltext=and&searchid=1&FIRSTINDEX=0&sortspec=relevance&volume=14&firstpage=988&resourcetype=HWCIT">GeneWise</a>. Mouse UniProtKB prot. 1
#157 Mono_ab_initio_RepeatMask Interspersed repeats and low complexity sequence identified by <a rel="external" href="http://www.repeatmasker.org/">RepeatMasker</a> using ab initio repeat profiles specific to Monodelphis. Repeats (Recon) 1
158 Prints Protein fingerprints (groups of conserved motifs) are aligned to the genome. These motifs come from the <a rel="external" href="http://nar.oxfordjournals.org/cgi/content/abstract/31/1/400?maxtoshow=&HITS=10&hits=10&RESULTFORMAT=1&author1=Attwood&andorexacttitle=and&andorexacttitleabs=and&andorexactfulltext=and&searchid=1&FIRSTINDEX=0&sortspec=relevance&resourcetype=HWCIT">PRINTS</a> database. Prints domain 1 {'type'=>'domain'}
159 mature_peptide Feature imported from <a rel="external" href="http://www.flybase.org">FlyBase</a>. Mature Peptide 1
160 aedes_cdna_est ESTs and cDNAs from Aedes placed on the genome with Exonerate EST 1 {'type' => 'cdna','default' => {'contigviewbottom' => 'stack'}}
161 EG3_Hs Evolutionary conserved regions ("Ecores") are inferred from alignments of the Human and Tetraodon genomes by <a rel="external" href="http://www.nature.com/ng/journal/v25/n2/abs/ng0600_235.html">Exofish, H. Roest Crollius et al.,</a> and grouped into contiguous, consistent sets ("Ecotigs") Human Ecores 1 {'default' => {'contigviewbottom' => 'stack'}}
162 DrosophilaBlast WuBLASTX of genomic segments against FlyBase Drosophila protein set Drosophila BLAST 1
163 Expression_pattern This sequence has been shown to be expressed in situ hybridisation experiments. The complete expression data collection is hosted by <a href="http://zfin.org/cgi-bin/webdriver?MIval=aa-xpatselect.apg">ZFIN</a> Expression pattern 1 {'type'=>'est'}
164 drosophila_gold_cdna Drosophila melanogaster cDNA sequences from the Drosophila <a rel="external" href="http://www.fruitfly.org">Gold Collection</a> are aligned to the genome using <a rel="external" href="http://www.biomedcentral.com/1471-2105/6/31">Exonerate</a>. Fly gold cDNA 1 {'default' => {'contigviewbottom' => 'stack'},'type' => 'cdna'}
165 chicken_est Chicken 'Expressed Sequence Tags' (ESTs) from <a rel="external" href="http://www.ncbi.nlm.nih.gov/dbEST/">dbEST</a> are aligned to the genome using <a rel="external" href="http://www.biomedcentral.com/1471-2105/6/31">Exonerate</a>. Chicken EST 1 {'type'=>'est'}
166 platypus_454_cdna Platypus reads from 454 sequencing are aligned to the genome using <a rel="external" href="http://www.biomedcentral.com/1471-2105/6/31">Exonerate</a>. Sequence reads (454) 1 {'default' => {'contigviewbottom' => 'stack'},'type' => 'cdna'}
167 Expression_profile imported expression profiles from WormBase Expressionprofile 1
#168 Uniprot_vertebrate_mammal Mammalian proteins from the <a rel="external" href="http://uniprot.org">UniProtKB</a> database, positioned on the genome through BLASTP of Genscan-predicted mammalian peptides to UniProtKB proteins. mammal UniProt prot. 1
169 remaneiX C. remanei proteins aligned by WU-BlastX remaneiX 1
170 ipi_humanX Human IPR proteins aligned by WU-BlastX ipihumanX 1
171 Eponine Transcription start sites predicted by <a rel="external" href="http://www.sanger.ac.uk/Users/td2/eponine/">Eponine-TSS</a>. TSS (Eponine) 1
172 ensembl_projection Genes were predicted by projecting human Ensembl transcripts through a BLASTZ DNA alignment to the human genome Proj. human gene 1 {'label_key' => '[text_label] [display_label]','default' => {'contigviewbottom' => 'transcript_label','contigviewtop' => 'gene_label','cytoview' => 'gene_label','MultiTop' => 'gene_label','MultiBottom' => 'collapsed_label','alignsliceviewbottom' => 'as_collapsed_label'}}
173 insertion_site Feature imported from<a rel="external" href="http://www.flybase.org">FlyBase</a> gff files. Insertion site 1
174 SNAP Ab initio gene prediction by <a rel="external" href="http://www.biomedcentral.com/1471-2105/5/59">SNAP</a>, on genomic sequence alone. SNAP prediction 1
175 FirstEF First Exon Finder (<a rel="external" href="http://www.nature.com/ng/journal/v29/n4/full/ng780.html">First EF</a>) predicts positions of the first exons of transcripts, both coding and non-coding, using the sequence to identify features such as CpG islands and promoter regions. First EF 1
176 Smart Protein domains and motifs in the <a rel="external" href="http://nar.oxfordjournals.org/cgi/content/full/34/suppl_1/D257?maxtoshow=&HITS=10&hits=10&RESULTFORMAT=1&author1=letunic&andorexacttitle=and&andorexacttitleabs=and&andorexactfulltext=and&searchid=1&FIRSTINDEX=0&sortspec=relevance&fdate=1/1/2006&tdate=12/31/2006&resourcetype=HWCIT">SMART</a> database. SMART domain 1 {'type'=>'domain'}
177 WGA2Genes Alignment to a human Ensembl protein inferred by projecting through a BLASTZ DNA alignment to the human genome BLASTZ prot. 1
178 human_one2one_mus_orth Human ensembl transcripts that are <a href="/info/docs/compara/homology_method.html" class="cp-external">one-to-one orthologues</a> with mouse are aligned to the genome using <a rel="external" href="http://www.biomedcentral.com/1471-2105/6/31">Exonerate</a>. Human protein 1
#179 Mono_sup_RepeatMask Interspersed repeats and low complexity sequence identified by <a rel="external" href="http://www.repeatmasker.org/">RepeatMasker</a> using a supplemental repeat database specific to Monodelphis. Supp. Repeats (Recon) 1
180 CDM Tetraodon cDNAs were prepared from 7 adult tissues by Genoscope, and aligned using BLAST and EST2GENOME <a rel="externa" href="http://www.ncbi.nlm.nih.gov/pubmed/9283765?ordinalpos=2&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum">(R. Mott, Comput Appl Biosci. 1997 13:477-8)</a>. Tetraodon cDNA 1 {'default' => {'contigviewbottom' => 'stack'},'type' => 'cdna','key' => 'tetraodon_cdna','name' => 'Tetraodon cDNA'}
181 HOX HOX genes manually curated by <a rel="external" href="http://www.genoscope.cns.fr/spip/">Genoscope</a>. HOX gene 1 {'label' => '[text_label] [display_label]'}
182 brigpepX C. briggsae proteins aligned by WU-BlastX brigpepX 1
183 tRNA transfer RNA genes tRNA 1 {'caption' => 'Non-coding','name' => 'Worm non-coding genes','label_key' => '[text_label] [display_label]','default' => {'contigviewbottom' => 'transcript_label','contigviewtop' => 'gene_label','cytoview' => 'gene_label','MultiTop' => 'gene_label','MultiBottom' => 'collapsed_label','alignsliceviewbottom' => 'as_collapsed_label'},'key' => 'ncRNA'}
184 celegans_mrna Caenorhabditis elegans mRNA are aligned to the genome using <a rel="external" href="http://www.biomedcentral.com/1471-2105/6/31">Exonerate</a>. C.elegans cDNA 1 {'type' => 'rna','default' => {'contigviewbottom' => 'stack'}}
185 transposable_element_target_duplication Feature imported from <a rel="external" href="http://www.flybase.org">FlyBase</a>. TE target duplication 1
186 GeneFinder Ab initio prediction of protein coding genes by Genefinder (C. Wilson, L. Hilyer, and P. Green, unpublished). Genefinder prediction 1
187 guineapig_est Guineapig 'Expressed Sequence Tags' (ESTs) from the <a rel="external" href="http://www.ebi.ac.uk/embl/">EMBL</a> database are aligned to the genome using <a rel="external" href="http://www.biomedcentral.com/1471-2105/6/31">Exonerate</a>. Guineapig EST 1 {'type'=>'est'}
188 medaka_protein Medaka proteins from <a rel="external" href="http://uniprot.org">UniProtKB</a> are aligned to the genome using <a rel="external" href="http://genome.cshlp.org/cgi/content/abstract/14/5/988?maxtoshow=&HITS=10&hits=10&RESULTFORMAT=&andorexactfulltext=and&searchid=1&FIRSTINDEX=0&sortspec=relevance&volume=14&firstpage=988&resourcetype=HWCIT">GeneWise</a>. Medaka UniProtKB prot. 1
189 Pseudogene Pseudogenes are identified from the Ensembl <a href="/info/docs/genebuild/genome_annotation.html" class="cp-external">gene set</a> (predicted by <a rel="external" href="http://genome.cshlp.org/cgi/content/abstract/14/5/988?maxtoshow=&HITS=10&hits=10&RESULTFORMAT=&andorexactfulltext=and&searchid=1&FIRSTINDEX=0&sortspec=relevance&volume=14&firstpage=988&resourcetype=HWCIT">GeneWise</a>/Exonerate) on the basis of frameshifted introns (introns of less than 10bp) and intron repeat content (introns of more than 80% repeat). See <a href="/info/docs/genebuild/genome_annotation.html#Other" class="cp-external">article</a> for more. Pseudogene 1 {'label_key' => '[text_label] [display_label]','default' => {'contigviewbottom' => 'transcript_label','contigviewtop' => 'gene_label','cytoview' => 'gene_label','MultiTop' => 'gene_label','MultiBottom' => 'collapsed_label','alignsliceviewbottom' => 'as_collapsed_label'}}
190 RepeatMask <a rel="external" href="http://www.repeatmasker.org">RepeatMasker</a> is used to find repeats and low-complexity sequences. This track usually shows repeats alone (not low-complexity sequences). Repeats 1
191 Uniprot_vertebrate_non_mammal Non-mammal proteins from the <a rel="external" href="http://uniprot.org">UniProtKB</a> database, positioned on the genome through BLASTP of Genscan-predicted (non-mammalian) peptides to UniProtKB proteins. non-mammal vertebrate UniProt prot. 1
192 Supp_RepeatMask Interspersed repeats and low complexity sequence identified by <a rel="external" href="http://www.repeatmasker.org">RepeatMasker</a> using a supplemental repeat database specific to the species. Supp. Repeats (Recon) 1
193 ipi_humanP Human IPR proteins aligned by WU-BlastX ipihumanP 1 {'type'=>'alignment'}
194 kyotograil_2005 C. intestinalis gene models from the <a rel="external" href="http://ghost.zool.kyoto-u.ac.jp/indexr1.html">KYOTOGRAIL set, version 2005,</a> aligned to the genome using <a rel="external" href="http://www.biomedcentral.com/1471-2105/6/31">Exonerate</a>. Kyotograil 05 prediction 1 {'type'=>'est'}
195 fish_protein Fish proteins aligned to the genome using GeneWise (E. Birney et al., Genome Res. 2004 14:988-95) Fish protein 1
196 brigpepP C. briggsae proteins aligned by WU-BlastP brigpepP 1 {'type'=>'alignment'}
197 protein_binding_site Feature imported from <a rel="external" href="http://www.flybase.org">FlyBase</a>. Protein Binding Site 1
198 Genscan Ab initio prediction of protein coding genes by <a rel="external" href="http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6WK7-45VGF7T-9&_user=776054&_rdoc=1&_fmt=&_orig=search&_sort=d&view=c&_version=1&_urlVersion=0&_userid=776054&md5=aa15a5f8122912c172ddb9dd15b237dc">Genscan</a>. The splice site models used are described in more detail in C. Burge, Modelling dependencies in pre-mRNA splicing signals. 1998 In Salzberg, S., Searls, D. and Kasif, S., eds. Computational Methods in Molecular Biology, Elsevier Science, Amsterdam, 127-163. Genscan prediction 1
200 slimswissprotX Swissprot proteins aligned by WU-BlastX slimswissprotX 1
201 aberration_junction Feature imported from <a rel="external" href="http://www.flybase.org">FlyBase</a>. Aberration junction 1
202 human_protein Human proteins from <a rel="external" href="http://uniprot.org">UniProtKB</a> used in the <a href="/info/docs/genebuild/index.html" class="cp-external">genebuild</a> are aligned to the genome using <a rel="external" href="http://genome.cshlp.org/cgi/content/abstract/14/5/988?maxtoshow=&HITS=10&hits=10&RESULTFORMAT=&andorexactfulltext=and&searchid=1&FIRSTINDEX=0&sortspec=relevance&volume=14&firstpage=988&resourcetype=HWCIT">GeneWise</a>. Human UniProt prot. 1
203 singapore_protein Protein-based gene-prediction Singapore gene 1 {'label' => '[text_label] [display_label]','key' => 'singapore_est',protein_align_feature' => {'do_not_display' => 1}}
204 slimtremblP TrEMBL proteins aligned by WU-BlastP slimtremblP 1 {'type'=>'alignment'}
205 UniGene Positions of <a rel="external" href="http://ncbi.nlm.nih.gov/UniGene/">UniGene</a> sequences along the genome. These are determined using TBLASTN of Genscan predictions against UniGene sequences. Unigene EST cluster 1 {'type' =>'cdna','default'=>{'contigviewbottom' => 'stack'}}
206 jgi_v1 Alignments to Ciona intestinalis gene models predicted by <a rel="external" href="http://www.jgi.doe.gov/genome-projects/">JGI</a> on <a rel="external" href="http://www.sciencemag.org/cgi/content/full/298/5601/2157">assembly version 1.0</a>. JGI v1 prediction 1
207 flybase Feature imported from <a rel="external" href="http://www.flybase.org">FlyBase</a>. FlyBase feature 1 {'label_key' => '[text_label] [display_label]','default' => {'contigviewbottom' => 'transcript_label','contigviewtop' => 'gene_label','cytoview' => 'gene_label','MultiTop' => 'gene_label','MultiBottom' => 'collapsed_label','alignsliceviewbottom' => 'as_collapsed_label'}}
208 anopheles_protein Anopheles proteins from UniProtKB and community gene databases aligned to the genome using GeneWise (E.Birney et al., Genome Res. 2004 14:988-95) Anopheles prot. 1 209 AedesBlast WuBLASTX of genomic segments against VB EST-supported Aedes protein set Aedes BLAST 1
210 SGD Genes annotated by <a href="http://www.yeastgenome.org/">SGD</a> and imported into Ensembl., SGD gene 1
211 xtrop_EST Xenopus tropicalis 'Expressed Sequence Tags' (ESTs) from <a rel="external" href="http://www.ncbi.nlm.nih.gov/dbEST/">dbEST</a> are aligned to the genome using <a rel="external" href="http://www.biomedcentral.com/1471-2105/6/31">Exonerate</a>. X.tropicalis EST 1 {'type'=>'est'}
212 tmhmm Prediction of transmembrane helices in proteins by <a rel="external" href="http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6WK7-457D7V9-K&_user=776054&_rdoc=1&_fmt=&_orig=search&_sort=d&view=c&_version=1&_urlVersion=0&_userid=776054&md5=a113464457fa5206c6699b9d464cbfee">TMHMM</a>. Transmembrane helices 1
213 mus_one2one_human_orth Mouse ensembl transcripts that are <a href="/info/docs/compara/homology_method.html" class="cp-external">one-to-one orthologues</a> with human are aligned to the genome using <a rel="external" href="http://www.biomedcentral.com/1471-2105/6/31">Exonerate</a>. Mouse protein 1
214 orangutan_cdna Orangutan cDNAs from RefSeq and EMBL aligned to the genome using Exonerate (G. Slater et al., BMC Bioinformatics. 2005 6:31) Orangutan cDNA 1 {'default' => {'contigviewbottom' => 'stack'},'type' => 'cdna'}
215 Uniprot_TR Proteins from the <a rel="external" href="http://uniprot.org">UniProtKB TrEMBL</a> database, aligned to the genome. TrEMBL prot. 1
216 EverythingBlast Proteins placed on the genome with BLASTX All BLAST 1
217 tetraodon_cdna Tetraodon cDNAs from <a rel="external" href="http://www.ebi.ac.uk/embl/">EMBL</a> and <a rel="external" href="http://www.ncbi.nlm.nih.gov/Genbank/">Genbank</a> are aligned to the genome using <a rel="external" href="http://www.biomedcentral.com/1471-2105/6/31">Exonerate</a>. Tetraodon cDNA 1 {'default' => {'contigviewbottom' => 'stack'},'type' => 'cdna','key' => 'tetraodon_cdna','name' => 'Tetraodon cDNA'}
#218 Tenrec_sup_RepeatMask Interspersed repeats and low complexity sequence identified by <a rel="external" href="http://www.repeatmasker.org">RepeatMasker</a> using a supplemental repeat database specific to Echinops telfairi. Supp. Repeats (Recon) 1
219 ARRAY_EMBL_MMC1_20k_v1 Vectorbase probe alignments: EMBL_MMC1_20k_v1 OLIGO EMBL_MMC1_20k_v1 1
220 platypus_est Platypus 'Expressed Sequence Tags' (ESTs) from <a rel="external" href="http://www.ebi.ac.uk/embl/">EMBL</a> are aligned to the genome using <a rel="external" href="http://www.biomedcentral.com/1471-2105/6/31">Exonerate</a>. Platypus EST 1 {'type'=>'est'}
221 Signalp Prediction of signal peptide cleavage sites by <a rel="external" href="http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6WK7-4CKBS0M-3&_user=776054&_coverDate=07%2F16%2F2004&_alid=772330061&_rdoc=1&_fmt=high&_orig=search&_cdi=6899&_sort=d&_docanchor=&view=c&_ct=1&_acct=C000042238&_version=1&_urlVersion=0&_userid=776054&md5=9f42be939814b7711268fd414604c9dd">SignalP</a>. Cleavage site (Signalp) 1
222 ensembl_IG_gene Immunoglobulin (Ig) and T-cell receptor (TcR) genes were imported from the <a rel="external" href="http://nar.oxfordjournals.org/cgi/content/full/33/suppl_1/D593?maxtoshow=&HITS=10&hits=10&RESULTFORMAT=1&author1=Lefranc&andorexacttitle=and&andorexacttitleabs=and&andorexactfulltext=and&searchid=1&FIRSTINDEX=0&sortspec=relevance&resourcetype=HWCIT">IMGT</a> database using <a rel="external" href="http://www.biomedcentral.com/1471-2105/6/31">Exonerate</a>. Ig/T-cell receptor gene 1 {'colour_key' => '[biotype]','caption' => 'Ensembl/Havana Ig gene','name' => 'Merged Ensembl and Havana Ig/T-cell receptor genes','label_key' => '[text_label] [display_label]','default' => {'MultiTop' => 'gene_label','contigviewbottom' => 'transcript_label','MultiBottom' => 'collapsed_label','contigviewtop' => 'gene_label','alignsliceviewbottom' => 'as_collapsed_label','cytoview' => 'gene_label'},'multi_caption' => 'Ensembl IG genes, or Merged Ensembl and Havana IG genes','key' => 'ensembl_IG_gene'}
223 horse_cdna Horse cDNAs from <a rel="external" href="http://www.ncbi.nlm.nih.gov/RefSeq/">NCBI RefSeq</a> and <a rel="external" href="http://www.ebi.ac.uk/embl/">EMBL</a> are aligned to the genome using <a rel="external" href="http://www.biomedcentral.com/1471-2105/6/31">Exonerate</a>. Horse cDNA 1 {'gene' => {'type' => 'cdna','default' => {'contigviewbottom' => 'stack'}}
224 horse_protein Horse protein sequences from <a rel="external" href="http://uniprot.org">UniProtKB</a> and <a rel="external" href="http://www.ncbi.nlm.nih.gov/RefSeq/">NCBI RefSeq</a> are aligned to the genome using <a rel="external" href="http://genome.cshlp.org/cgi/content/abstract/14/5/988?maxtoshow=&HITS=10&hits=10&RESULTFORMAT=&andorexactfulltext=and&searchid=1&FIRSTINDEX=0&sortspec=relevance&volume=14&firstpage=988&resourcetype=HWCIT">GeneWise</a>. Horse prot. 1
225 Est2genome_human Alignment of human ESTs (expressed sequence tags) to the genome using the program <a rel="external" href="http://emboss.sourceforge.net/apps/cvs/emboss/apps/est2genome.html">Est2genome</a>. ESTs are from <a rel="external" href="http://www.ncbi.nlm.nih.gov/dbEST/">dbEST</a> Human EST (EST2genome) 1 {'type'=>'est'}
226 Est2genome_mouse Alignment of mouse ESTs (expressed sequence tags) to the genome using the program <a rel="external" href="http://emboss.sourceforge.net/apps/cvs/emboss/apps/est2genome.html">Est2genome</a>. ESTs are from <a rel="external" href="http://www.ncbi.nlm.nih.gov/dbEST/">dbEST</a> Mouse EST (EST2genome) 1 {'type'=>'est'}
227 wormpepP C. elegans proteins aligned by WU-BlastP wormpepP 1 {'type'=>'alignment'}
228 Seg Identification of peptide low complexity sequences by <a rel="external" href="http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6TFV-44PXMF3-45&_user=776054&_coverDate=06%2F30%2F1993&_rdoc=6&_fmt=high&_orig=browse&_srch=doc-info(%23toc%235236%231993%23999829997%23279143%23FLP%23display%23Volume)&_cdi=5236&_sort=d&_docanchor=&_ct=13&_acct=C000042238&_version=1&_urlVersion=0&_userid=776054&md5=ac6f98882f2c6626643118367fb28cad">Seg</a>. Low complexity (Seg) 1
229 vectorbase Genes were annotated by merging Ensembl and TIGR predictions sets. Ensembl automatic analysis pipeline using either a GeneWise/Exonerate model from a database protein or a set of aligned cDNAs/ESTs followed by an ORF prediction. GeneWise/Exonerate models are further combined with available aligned cDNAs/ESTs to annotate UTRs (For more information see V.Curwen et al., Genome Res. 2004 14:942-50). TIGR annotations were modeled based on a combination of Augustus (M. Stanke), GlimmerHMM (M. Pertea), Genie (D. Kulp), and Twinscan (M. Brent) gene predictions, coupled with protein and EST genome alignments. VectorBase gene 1 {'label_key' => '[text_label] [display_label]','default' => {'contigviewbottom' => 'transcript_label','contigviewtop' => 'gene_label','cytoview' => 'gene_label'}}
230 Fgenesh Ab initio prediction of protein coding genes, based on the genomic sequence alone <a rel="external" href="http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=10779491">AA Salamov et al., Genome Res. 2000 4:516-22</a>. FGENESH prediction 1
231 medaka_est Medaka 'Expressed Sequence Tags' (ESTs) from <a rel="external" href="http://www.ncbi.nlm.nih.gov/dbEST/">dbEST</a> are aligned to the genome using <a rel="external" href="http://www.biomedcentral.com/1471-2105/6/31">Exonerate</a>. Medaka EST 1 {'type'=>'est'}
232 rodent_protein Rodent Proteins from <a rel="external" href="http://www.ncbi.nlm.nih.gov/RefSeq/">NCBI RefSeq</a> and <a rel="external" href="http://uniprot.org">UniProtKB/TrEMBL</a> are aligned to the genome using <a rel="external" href="http://genome.cshlp.org/cgi/content/abstract/14/5/988?maxtoshow=&HITS=10&hits=10&RESULTFORMAT=&andorexactfulltext=and&searchid=1&FIRSTINDEX=0&sortspec=relevance&volume=14&firstpage=988&resourcetype=HWCIT">GeneWise</a>. Rodent RefSeq/TrEMBL prot. 1
233 deletion Feature imported from <a rel="external" href="http://www.flybase.org">FlyBase</a>. Deletion 1
234 xtrop_cDNA Xenopus tropicalis cDNAs from <a rel="external" href="http://www.ncbi.nlm.nih.gov/RefSeq/">NCBI RefSeq</a> and <a rel="external" href="http://www.ebi.ac.uk/embl/">EMBL</a> are aligned to the genome using <a rel="external" href="http://www.biomedcentral.com/1471-2105/6/31">Exonerate</a>. X.tropicalis cDNA 1 {'type' => 'cdna','default' => {'contigviewbottom' => 'stack'}}
235 remaneiP C. remanei proteins aligned by WU-BlastP remaneiP 1 {'type'=>'alignment'}
236 genscan Ab initio prediction of protein coding genes by <a rel="external" href="http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6WK7-45VGF7T-9&_user=776054&_rdoc=1&_fmt=&_orig=search&_sort=d&view=c&_version=1&_urlVersion=0&_userid=776054&md5=aa15a5f8122912c172ddb9dd15b237dc">Genscan</a>. The splice site models used are described in more detail in C. Burge, Modelling dependencies in pre-mRNA splicing signals. 1998 In Salzberg, S., Searls, D. and Kasif, S., eds. Computational Methods in Molecular Biology, Elsevier Science, Amsterdam, 127-163. Genscan prediction 1
237 Arma_sup_RepeatMask Interspersed repeats and low complexity sequence identified by <a rel="external" href="http://www.repeatmasker.org/">RepeatMasker</a> using a supplemental repeat database specific to Dasypus novemcinctus. Supp. Repeats (Recon) 1
238 fugu_protein Takifugu proteins from <a rel="external" href="http://uniprot.org">UniProtKB</a> are aligned to the genome using <a rel="external" href="http://genome.cshlp.org/cgi/content/abstract/14/5/988?maxtoshow=&HITS=10&hits=10&RESULTFORMAT=&andorexactfulltext=and&searchid=1&FIRSTINDEX=0&sortspec=relevance&volume=14&firstpage=988&resourcetype=HWCIT">GeneWise</a>. Takifugu prot. 1
239 rescue_fragment Feature (Fly) imported from <a rel="external" href="http://www.flybase.org">FlyBase</a>. Rescue Fragment 1
240 ccds Protein coding sequences agreed upon by the Consensus Coding Sequence project, or <a href="/info/docs/genebuild/ccds.html" class="cp-external">CCDS</a>. CCDS set 1 {'default' => {'contigviewbottom' => 'normal'},'type' => 'cdna'}
241 ARRAY_JHSPH_AG_GAMBER_15k_v1 Vectorbase probe alignments: JHSPH_AG_GAMBER_15k_v1 OLIGO JHSPH_AG_GAMBER_15k_v1 1
242 slimtremblX TrEMBL proteins aligned by WU-BlastX slimtremblX 1
243 transposable_element_insertion Feature imported from FlyBase (http://www.flybase.org) TE insertion site 1
244 FANTOM_GIS_PET These are short sequence tags from the start sites of polyA transcripts. These ditags were downloaded from the <a rel="external" href="http://fantom.gsc.riken.go.jp/">Riken Fantom</a> project and aligned to the genome using <a rel="external" href="http://www.biomedcentral.com/1471-2105/6/31">Exonerate</a>. Fantom GIS ditags 1
#245 Stick_sup_RepeatMask Interspersed repeats and low complexity sequence identified by <a rel="external" href="http://www.repeatmasker.org">RepeatMasker</a> using a supplemental repeat database specific to Gasterosteus aculeatus. Supp. Repeats (Recon) 1
246 Operon Multi-gene feature imported from <a rel="external" href="http://www.wormbase.org">Wormbase</a> annotation. Operon 1
247 platypus_cdna Platypus cDNAs from <a rel="external" href="http://www.ncbi.nlm.nih.gov/RefSeq/">NCBI RefSeq</a> and <a rel="external" href="http://www.ebi.ac.uk/embl/">EMBL</a> are aligned to the genome using <a rel="external" href="http://www.biomedcentral.com/1471-2105/6/31">Exonerate</a>. Platypus cDNA 1 {'default' => {'contigviewbottom' => 'stack'},'type' => 'cdna'}
248 RepeatMasker_TIGR Interspersed repeats identified by RepeatMasker (http://www.repeatmasker.org/) RepeatMask 1
249 ensembl_havana_transcript Transcript where the Ensembl genebuild transcript and the <a rel="external" href="http://vega.sanger.ac.uk/index.html">Vega</a> manual annotation have the same sequence, for every base pair. See <a href="/info/docs/genebuild/genome_annotation.html" class="cp-external">article</a>. Ensembl/Havana merge transcript 1 {'colour_key' => '[biotype]_[status]','caption' => 'Ensembl/Havana gene','name' => 'Merged Ensembl and Havana Genes','label_key' => '[text_label] [display_label]','default' => {'contigviewbottom' => 'transcript_label','contigviewtop' => 'gene_label','cytoview' => 'gene_label','MultiTop' => 'gene_label','MultiBottom' => 'collapsed_label','alignsliceviewbottom' => 'as_collapsed_label'},'key' => 'ensembl','multi_caption' => 'Ensembl genes, or Merged Ensembl and Havana genes'}
250 Uniprot_mammal Mammalian proteins from the <a rel="external" href="http://uniprot.org">UniProtKB</a> database, positioned on the genome through BLASTP of Genscan-predicted mammalian peptides to UniProtKB proteins. mammal UniProt prot. 1
251 fosmid Vancouver fosmids mapped to the C.elegans genome (available through GeneService) fosmid 1
252 CYT Cytokine gene, structure manually curated by Genoscope, Cytokine gene 1 {'label' => '[text_label] [display_label]'}
253 dog_est Dog 'Expressed Sequence Tags' (ESTs) from <a rel="external" href="http://www.ncbi.nlm.nih.gov/dbEST/">dbEST</a> are aligned to the genome using <a rel="external" href="http://www.biomedcentral.com/1471-2105/6/31">Exonerate</a>. Dog EST 1 {'type'=>'est'}
254 Unigene Positions of <a rel="external" href="http://ncbi.nlm.nih.gov/UniGene/">UniGene</a> sequences along the genome. These are determined using TBLASTN of Genscan predictions against UniGene sequences. Unigene EST cluster 1 {'type' => 'cdna'}
255 stickleback_EST Gasterosteus aculeatus 'Expressed Sequence Tags' (ESTs) from <a rel="external" href="http://www.ncbi.nlm.nih.gov/dbEST/">dbEST</a> are aligned to the genome using <a rel="external" href="http://www.biomedcentral.com/1471-2105/6/31">Exonerate</a>. Stickleback EST 1 {'type'=>'est'}
256 mammal_protein Mammalian proteins from <a rel="external" href="http://uniprot.org">UniProtKB</a> are aligned to the genome using <a rel="external" href="http://genome.cshlp.org/cgi/content/abstract/14/5/988?maxtoshow=&HITS=10&hits=10&RESULTFORMAT=&andorexactfulltext=and&searchid=1&FIRSTINDEX=0&sortspec=relevance&volume=14&firstpage=988&resourcetype=HWCIT">GeneWise</a>. Mammal UniProt prot. 1
257 snap Ab initio gene prediction by <a rel="external" href="http://www.biomedcentral.com/1471-2105/5/59">SNAP</a>, on genomic sequence alone. SNAP prediction 1
258 rat_est Rattus norvegicus 'Expressed Sequence Tags' (ESTs) from <a rel="external" href="http://www.ncbi.nlm.nih.gov/dbEST/">dbEST</a> are aligned to the genome using <a rel="external" href="http://www.biomedcentral.com/1471-2105/6/31">Exonerate</a>. Rat EST 1 {'type'=>'est','gene' => {'do_not_display' => '1'}}
259 ost Caenorhabditis elegans OSTs of the Vidal Lab aligned to the genome using BLAT C.elegans OST 1 {'dna_align_feature' => {'do_not_display' => '1'},'type' => 'est'}
260 guineapig_protein Guineapig protein sequences from Swiss-Prot/TrEMBL and RefSeq aligned to the genome using GeneWise (E. Birney et al., Genome Res. 2004 14:988-95) Guineapig protein 1
261 marker Markers, or sequence tagged sites (STS), from <a rel="external" href="http://www.ncbi.nlm.nih.gov/sites/entrez?db=unists">UniSTS</a> are aligned to the genome using <a rel="external" href="http://genome.cshlp.org/cgi/content/full/7/5/541">Electronic PCR (e-PCR)</a>. Marker 1
262 ArthropodaBlast Proteins placed on the genome with BLASTX Arthropoda BLAST 1
263 nembase_contig NemBase EST contigs nembasecontig 1
264 estgene ESTs are mapped on the genome using <a rel="external" href="http://www.biomedcentral.com/1471-2105/6/31">Exonerate</a>. Genes (including isoforms) are inferred using the <a rel="external" href="http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=479129&rendertype=abstract">Cluster-Merge algorithm</a>. EST-based gene 1 {'label' => '[text_label] [display_label]'}
265 stickleback_cDNA Gasterosteus aculeatus cDNAs from <a rel="external" href="http://www.ncbi.nlm.nih.gov/RefSeq/">NCBI RefSeq</a> and <a rel="external" href="http://www.ebi.ac.uk/embl/">EMBL</a> are aligned to the genome using <a rel="external" href="http://www.ebi.ac.uk/~guy/exonerate/">Exonerate</a>. Stickleback cDNA 1 {'default' => {'contigviewbottom' => 'stack'},'type' => 'cdna'}
266 DipteraBlast Proteins placed on the genome with BLASTX Diptera BLAST 1
267 EG3_Mm Evolutionary conserved regions ("Ecores") are inferred from alignments of the Mouse and Tetraodon genomes by <a rel="external" href="http://www.nature.com/ng/journal/v25/n2/abs/ng0600_235.html">Exofish, H. Roest Crollius et al.,</a> and grouped into contiguous, consistent sets ("Ecotigs") Mouse Ecores 1 {'default' => {'contigviewbottom' => 'stack'}}
268 enhancer Feature imported from <a rel="external" href="http://www.flybase.org">FlyBase</a>. Enhancer 1
269 zfish_cDNA Danio rerio cDNAs from <a rel="external" href="http://www.ncbi.nlm.nih.gov/RefSeq/">NCBI RefSeq</a> and <a rel="external" href="http://www.ebi.ac.uk/embl/">EMBL</a> are aligned to the genome using <a rel="external" href="http://www.biomedcentral.com/1471-2105/6/31">Exonerate</a>. Zebrafish cDNA 1 {'type' => 'cdna','default' => {'contigviewbottom' => 'stack'}}
270 PercentageRepeat Percentage of repetitive elements for top level sequences (such as chromosomes, scaffolds, etc.) Repeats (percent) 1
271 CHIP_PET Positions of mRNA start and end sequences are shown here, obtained by paired-end ditag (PET) sequencing on ChIP (chromatin immunoprecipitation) <a href="/Homo_sapiens_ditags/CHIP_PET.html">samples</a>. Ditags (ChIP-PET) 0
272 XrefExonerateProtein match Protein 0
273 CollapseAffy 0
274 FANTOM_GIS_PET_raw These are short sequence tags from the start sites of polyA transcripts. These ditags were downloaded from the <a rel="external" href="http://fantom.gsc.riken.go.jp/">Riken Fantom</a> project and aligned to the genome using <a rel="external" href="http://www.biomedcentral.com/1471-2105/6/31">Exonerate</a>. FANTOM GIS ditags raw 0
275 XrefCoordinateMapping 0
276 exonerate_IG_gene Immunoglobulin (Ig) and T-cell receptor (TcR) genes were imported from the <a rel="external" href="http://nar.oxfordjournals.org/cgi/content/full/33/suppl_1/D593?maxtoshow=&HITS=10&hits=10&RESULTFORMAT=1&author1=Lefranc&andorexacttitle=and&andorexacttitleabs=and&andorexactfulltext=and&searchid=1&FIRSTINDEX=0&sortspec=relevance&resourcetype=HWCIT">IMGT</a> database using <a rel="external" href="http://www.biomedcentral.com/1471-2105/6/31">Exonerate</a>. Ig and TcR transcripts 0 {'type' => 'cdna'}
277 CHIP_PET_raw Raw data for ChIP_PET <a href="/Homo_sapiens_ditags/CHIP_PET.html">sample</a> alignments. 0
278 manual_models Manually curated transcript models made by VB manual_models 0 279 Exonerate_segment Immunoglubulin (Ig) and T-cell receptor (TcR) genes are imported from the <a rel="external" href="http://imgt.cines.fr">IMGT database</a> and aligned to the genome using <a rel="external" href="http://www.biomedcentral.com/1471-2105/6/31">Exonerate</a>. See <a href="/info/docs/genebuild/ig_tcr.html" class="cp-external">article</a>. Ig/T-cell receptor gene 0 {'type' => 'cdna'}
280 MergedByHuman 0
281 TargettedGenewise 0
282 GIS_PET_raw Raw data. See <a href="/Homo_sapiens_ditags/GIS_PET.html">method</a> described here. Ditags (GIS raw) 0
283 FANTOM_GSC_PET_raw These are short sequence tags from the start sites of polyA transcripts. These ditags were downloaded from the <a rel="external" href="http://fantom.gsc.riken.go.jp/">Riken Fantom</a> project and aligned to the genome using <a rel="external" href="http://www.biomedcentral.com/1471-2105/6/31">Exonerate</a>. Fantom GSC raw 0
284 AlignOligoProbes Microarray probes aligned to the genome, if probe sequences are provided by the manufacturer. Aligned oligo 0
285 GIS_PET_Encode See <a href="/Homo_sapiens_ditags/GIS_PET.html">method</a> described here. Ditags (GIS Encode) 0
286 cdna_exonerate cDNA sequences are mapped onto the genome using <a rel="external" href="http://www.biomedcentral.com/1471-2105/6/31">Exonerate</a>. cDNA 1 {'default' => {'contigviewbottom' => 'stack'},'type' => 'cdna'}
287 SimilarityGenewise 0
288 community_models Community provided transcript models from VB community_models 0
289 steve_human_cdna 0
290 BeeBlast WuBLASTX of genomic segments against Bee protein set BLAST Bee 0
291 XrefExonerateDNA Sequences from various databases are matched to Ensembl transcripts using <a rel="external" href="http://www.biomedcentral.com/1471-2105/6/31">Exonerate</a>. These are external references, or 'Xrefs'. DNA match 0
292 steve_mouse_cdna 0
293 ExtendedByHuman 0
294 est_support_estgenes ESTs and cDNAs aligned to the genome using Exonerate (G. Slater et al., BMC Bioinformatics. 2005 6:31) and used as support for estgenes EST support estgenes 0 {'type'=>'est'}
295 refseq_human 0
296 HumanOrthologue 0
297 ExtendedByMedaka 0
298 GIS_PET Positions of mRNA start and end sequences are shown here, obtained by paired-end ditag (PET) sequencing by GIS (Genome Institute of Singapore). <a href="/Homo_sapiens_ditags/GIS_PET.html">Method</a> described here. Ditags (GIS) 0
300 green_anole_est Green anole 'Expressed Sequence Tags' (ESTs) from <a rel="external" href="http://www.ncbi.nlm.nih.gov/dbEST/">dbEST</a> are aligned to the genome using <a rel="external" href="http://www.biomedcentral.com/1471-2105/6/31">Exonerate</a>. Green anole EST 1 {'type'=>'est'}
301 green_anole_cdna Green anole cDNAs from <a rel="external" href="http://www.ncbi.nlm.nih.gov/RefSeq/">NCBI RefSeq</a> and <a rel="external" href="http://www.ebi.ac.uk/embl/">EMBL</a> are aligned to the genome using <a rel="external" href="http://www.biomedcentral.com/1471-2105/6/31">Exonerate</a>. Green anole cDNA 1 {'default' => {'contigviewbottom' => 'stack'},'type' => 'cdna'}
302 green_anole_protein Green anole proteins from <a rel="external" href="http://uniprot.org">UniProtKB</a> are aligned to the genome using <a rel="external" href="http://genome.cshlp.org/cgi/content/abstract/14/5/988?maxtoshow=&HITS=10&hits=10&RESULTFORMAT=&andorexactfulltext=and&searchid=1&FIRSTINDEX=0&sortspec=relevance&volume=14&firstpage=988&resourcetype=HWCIT">GeneWise</a>. Green anole UniProtKB prot. 1
303 ensembl_chicken_protein Chicken protein sequences from <a rel="external" href="http://www.ensembl.org">Ensembl</a> are aligned to the genome using <a rel="external" href="http://www.biomedcentral.com/1471-2105/ 6/31">Exonerate</a>. Ensembl chicken protein 1
304 est_support_genes ESTs and cDNAs aligned to the genome using Exonerate (G. Slater et al., BMC Bioinformatics. 2005 6:31) and used as support for VectorBase genes EST support 1 {'type' => 'est','default' => {'contigviewbottom' => 'stack'}}
305 chicken_RepeatMask <a rel="external" href="http://www.repeatmasker.org">RepeatMasker</a> is used to find repeats and low-complexity sequences using a chicken repeat library. This track usually shows repeats alone (not low-complexity sequences). Repeats (Chicken) 1
306 zebra_finch_cdna Taeniopygia guttata cDNAs from <a rel="external" href="http://www.ncbi.nlm.nih.gov/RefSeq/">NCBI RefSeq</a> and <a rel="external" href="http://www.ebi.ac.uk/embl/">EMBL</a> are aligned to the genome using <a rel="external" href="http://www.biomedcentral.com/1471-2105/6/31">Exonerate</a>. Zebra finch cDNA 1 {'default' => {'contigviewbottom' => 'stack'},'type' => 'cdna'}
307 zebra_finch_est Taeniopygia guttata 'Expressed Sequence Tags' (ESTs) from <a rel="external" href="http://www.ncbi.nlm.nih.gov/dbEST/">dbEST</a> are aligned to the genome using <a rel="external" href="http://www.biomedcentral.com/1471-2105/6/31">Exonerate</a>. Zebra finch EST 1 {'type'=>'est'}
308 zebra_finch_protein Taeniopygia guttata protein sequences from <a rel="external" href="http://uniprot.org">UniProtKB</a> and <a rel="external" href="http://www.ncbi.nlm.nih.gov/RefSeq/">NCBI RefSeq</a> are aligned to the genome using <a rel="external" href="http://genome.cshlp.org/cgi/content/abstract/14/5/988?maxtoshow=&HITS=10&hits=10&RESULTFORMAT=&andorexactfulltext=and&searchid=1&FIRSTINDEX=0&sortspec=relevance&volume=14&firstpage=988&resourcetype=HWCIT">GeneWise</a>. Zebra finch UniProtKB prot. 1
309 marmoset_cdna Callithrix jacchus cDNAs from <a rel="external" href="http://www.ncbi.nlm.nih.gov/RefSeq/">NCBI RefSeq</a> and <a rel="external" href="http://www.ebi.ac.uk/embl/">EMBL</a> are aligned to the genome using <a rel="external" href="http://www.biomedcentral.com/1471-2105/6/31">Exonerate</a>. Marmoset cDNA 1 {'default' => {'contigviewbottom' => 'stack'},'type' => 'cdna'}
310 marmoset_est Callithrix jacchus 'Expressed Sequence Tags' (ESTs) from <a rel="external" href="http://www.ncbi.nlm.nih.gov/dbEST/">dbEST</a> are aligned to the genome using <a rel="external" href="http://www.biomedcentral.com/1471-2105/6/31">Exonerate</a>. Marmoset EST 1 {'type'=>'est'}
311 marmoset_protein Callithrix jacchus protein sequences from <a rel="external" href="http://uniprot.org">UniProtKB</a> and <a rel="external" href="http://www.ncbi.nlm.nih.gov/RefSeq/">NCBI RefSeq</a> are aligned to the genome using <a rel="external" href="http://genome.cshlp.org/cgi/content/abstract/14/5/988?maxtoshow=&HITS=10&hits=10&RESULTFORMAT=&andorexactfulltext=and&searchid=1&FIRSTINDEX=0&sortspec=relevance&volume=14&firstpage=988&resourcetype=HWCIT">GeneWise</a>. Marmoset UniProtKB prot. 1
312 swall Proteins from the <a rel="external" href="http://uniprot.org">UniProtKB Swiss-Prot</a> database, aligned to the genome. UniProt prot. 1
313 refseq_mouse Murine cDNAs from <a rel="external" href="http://www.ncbi.nlm.nih.gov/RefSeq/">NCBI RefSeq</a> are aligned to the genome using <a rel="external" href="http://genome.cshlp.org/cgi/content/abstract/14/5/988?maxtoshow=&HITS=10&hits=10&RESULTFORMAT=&andorexactfulltext=and&searchid=1&FIRSTINDEX=0&sortspec=relevance&volume=14&firstpage=988&resourcetype=HWCIT">GeneWise</a>. Mouse RefSeq cDNA 1 {'default' => {'contigviewbottom' => 'stack'},'type' => 'cdna'}
314 refseq_human Human cDNAs from <a rel="external" href="http://www.ncbi.nlm.nih.gov/RefSeq/">NCBI RefSeq</a> are aligned to the genome using <a rel="external" href="http://genome.cshlp.org/cgi/content/abstract/14/5/988?maxtoshow=&HITS=10&hits=10&RESULTFORMAT=&andorexactfulltext=and&searchid=1&FIRSTINDEX=0&sortspec=relevance&volume=14&firstpage=988&resourcetype=HWCIT">GeneWise</a>. Human RefSeq cDNA 1 {'default' => {'contigviewbottom' => 'stack'},'type' => 'cdna'}
315 refseq_zebrafish Zebrafish cDNAs from <a rel="external" href="http://www.ncbi.nlm.nih.gov/RefSeq/">NCBI RefSeq</a> are aligned to the genome using <a rel="external" href="http://genome.cshlp.org/cgi/content/abstract/14/5/988?maxtoshow=&HITS=10&hits=10&RESULTFORMAT=&andorexactfulltext=and&searchid=1&FIRSTINDEX=0&sortspec=relevance&volume=14&firstpage=988&resourcetype=HWCIT">GeneWise</a>. Zebrafish RefSeq cDNA 1 {'default' => {'contigviewbottom' => 'stack'},'type' => 'cdna'}
316 augustus Ab initio prediction of protein coding genes by Augustus, a software tool for gene prediction in eukaryotes based on a Generalized Hidden Markov Model. Stanke et al., Nucleic Acids Res., 34: W435-W439 (2006). Augustus prediction 1
317 RepeatMasker Interspersed repeats and low complexity sequence identified by <a rel="external" href="http://www.repeatmasker.org/">RepeatMasker</a> using ab initio repeat profiles specific to the species. Repeats (Recon) 1
318 polyA_signal PolyA signals identified during manual annotation PolyA Signal 1 {'strand'=>'b','transcript_associated'=>1}
319 pseudo_polyA Poly A like structures associated with pseudogenes Pseudo PolyA 1 {'strand'=>'b','transcript_associated'=>1}
320 RSS The IG and T-cell recombination signal sequences motifs are canonically considered to be nonamers and heptamers seperated by spacers of 12 or 23 nucleotides and are found at the 3' end of the V elements, the 5' end of the J elements, and on both sides of the D elements [ V(D)J recombination mechanism]. RSS Motif. 1 {'strand'=>'b','transcript_associated'=>1}
321 otter_eucomm Virtual mouse genes (produced for the <a rel="external" href="http://www.eucomm.org">EUCOMM</a> project) representing the gene structure produced after knockout of exons critical to gene function. KO gene (EUCOMM) 1 {'colour_key' => '[gene.logic_name]_[gene.biotype]'}
322 otter_komp Virtual mouse genes (produced for the <a rel="external" href="http://www.nih.gov/science/models/mouse/knockout/">KOMP</a> project) representing the gene structure produced after knockout of exons critical to gene function. KO gene (KOMP) 1 {'colour_key' => '[gene.logic_name]_[gene.biotype]'}
323 EUCOMM This mouse track is linked to the mouse Knockout gene track. It shows the locations of exons identified by Havana as being critical for correct translation of the longest transcript at a specific loci. Knockout Deletion 1 {'strand'=>'b','transcript_associated'=>1}
324 est2genome_fish Alignment of mouse ESTs (expressed sequence tags) to the genome using the program <a rel="external" href="http://emboss.sourceforge.net/apps/cvs/emboss/apps/est2genome.html">Est2genome</a>. ESTs are from <a rel="external" href="http://www.ncbi.nlm.nih.gov/dbEST/">dbEST</a> Zebrafish EST (EST2genome) 1 {'type'=>'est'}
325 PCodDensity Density of Vega protein coding genes Genes (density) 1
326 PTransDensity Density of Vega processed transcripts Genes (density) 1
327 PseudoGeneDensity Density of Vega pseudogenes Genes (density) 1
328 IGGeneDensity Density of Vega IG genes Genes (density) 1
329 TECGeneDensity Density of Vega TEC genes Genes (density) 1
330 FOSends End sequences of Fosmid library clones used in the sequencing project aligned to the genome using <a rel="external" href="http://www.sanger.ac.uk/Software/analysis/SSAHA2/">SSAHA2</a>. FOS ends 1 {'show_strands' => '1'}
331 Uniprot_vertebrate_non_mammal_pe_12 Non-mammal proteins from the <a rel="external" href="http://uniprot.org">UniProtKB</a> database, positioned on the genome through BLASTP of Genscan-predicted (non-mammalian) peptides to UniProtKB proteins. non-mammal UniProt prot. 1
332 Uniprot_vertebrate_non_mammal_pe_345 Non-mammal proteins from the <a rel="external" href="http://uniprot.org">UniProtKB</a> database, positioned on the genome through BLASTP of Genscan-predicted (non-mammalian) peptides to UniProtKB proteins. non-mammal UniProt prot. 1
#333 Uniprot_mammal_pe_12 Mammalian proteins from the <a rel="external" href="http://uniprot.org">UniProtKB</a> database, positioned on the genome through BLASTP of Genscan-predicted mammalian peptides to UniProtKB proteins. mammal UniProt prot. 1
#334 Uniprot_mammal_pe_345 Mammalian proteins from the <a rel="external" href="http://uniprot.org">UniProtKB</a> database, positioned on the genome through BLASTP of Genscan-predicted mammalian peptides to UniProtKB proteins. mammal UniProt prot. 1
335 Uniprot_primate Primate proteins from the <a rel="external" href="http://uniprot.org">UniProtKB</a> database, positioned on the genome through BLASTP of Genscan-predicted primate peptides to UniProtKB proteins. primate UniProt prot. 1
#336 Uniprot_primate2 Primate proteins from the <a rel="external" href="http://uniprot.org">UniProtKB</a> database, positioned on the genome through BLASTP of Genscan-predicted primate peptides to UniProtKB proteins. primate UniProt prot. 1
337 WGA2Genes_ContigAwareNet Alignment to a human Ensembl protein inferred by projecting through a BLASTZ DNA alignment to the human genome BLASTZ prot, using ContigAwareNet. Proj. human gene 1 {'key' => 'WGA2Genes_ContigAwareNet','name' => 'Proj. human gene'}
338 WGA2Genes_HiveChain Alignment to a human Ensembl protein inferred by projecting through a BLASTZ DNA alignment to the human genome BLASTZ prot, using HiveChain. Proj. human gene 1 {'key' => 'WGA2Genes_ContigAwareNet','name' => 'Proj. human gene'}
339 rat_cdna2genome Rattus norvegicus cDNAs from <a rel="external" href="http://www.ncbi.nlm.nih.gov/RefSeq/">NCBI RefSeq</a> and <a rel="external" href="http://www.ebi.ac.uk/embl/">EMBL</a> are aligned to the genome using <a rel="external" href="http://www.biomedcentral.com/1471-2105/6/31">Exonerate cnda2geome model</a>. Rat RefSeq/EMBL cdna2genome 0
340 pig_cdna Pig cDNAs from <a rel="external" href="http://www.ncbi.nlm.nih.gov/RefSeq/">NCBI RefSeq</a> and <a rel="external" href="http://www.ebi.ac.uk/embl/">EMBL</a> are aligned to the genome using <a rel="external" href="http://www.biomedcentral.com/1471-2105/6/31">Exonerate</a>. pig cDNA 1 {'type' => 'cdna','default' => {'contigviewbottom' => 'stack'}}
341 pig_est Pig 'Expressed Sequence Tags' (ESTs) from the <a rel="external" href="http://www.ebi.ac.uk/embl/">EMBL</a> database are aligned to the genome using <a rel="external" href="http://www.biomedcentral.com/1471-2105/6/31">Exonerate</a>. pig EST 1 {'type'=>'est'}
342 pig_protein Pig protein sequences from Swiss-Prot/TrEMBL and RefSeq aligned to the genome using GeneWise (E. Birney et al., Genome Res. 2004 14:988-95) pig protein 1
343 ensembl_havana_IG_gene Immunoglobulin (Ig) and T-cell receptor (TcR) genes where the Ensembl models build from the set imported from the <a rel="external" href="http://nar.oxfordjournals.org/cgi/content/full/33/suppl_1/D593?maxtoshow=&HITS=10&hits=10&RESULTFORMAT=1&author1=Lefranc&andorexacttitle=and&andorexacttitleabs=and&andorexactfulltext=and&searchid=1&FIRSTINDEX=0&sortspec=relevance&resourcetype=HWCIT">IMGT</a> database using <a rel="external" href="http://www.biomedcentral.com/1471-2105/6/31">Exonerate</a> overlap one of the gene models imported from the manually annotated IG gene set from the <a rel="external" href="http://www.sanger.ac.uk/HGP/havana/havana.shtml">Havana</a> project. Ig/T-cell receptor gene 1 {'colour_key' => '[biotype]','caption' => 'Ensembl/Havana Ig gene','name' => 'Merged Ensembl and Havana Ig/T-cell receptor genes','label_key' => '[text_label] [display_label]','default' => {'MultiTop' => 'gene_label','contigviewbottom' => 'transcript_label','MultiBottom' => 'collapsed_label','contigviewtop' => 'gene_label','alignsliceviewbottom' => 'as_collapsed_label','cytoview' => 'gene_label'},'multi_caption' => 'Ensembl IG genes, or Merged Ensembl and Havana IG genes','key' => 'ensembl_IG_gene'}
344 havana_IG_gene Immunoglobulin (Ig) and T-cell receptor (TcR) genes imported from the manually annotated IG gene set from the <a rel="external" href="http://www.sanger.ac.uk/HGP/havana/havana.shtml">Havana</a> project. Havana gene 1 {'colour_key' => '[biotype]','caption' => 'Ensembl/Havana Ig gene','name' => 'Merged Ensembl and Havana Ig/T-cell receptor genes','label_key' => '[text_label] [display_label]','default' => {'MultiTop' => 'gene_label','contigviewbottom' => 'transcript_label','MultiBottom' => 'collapsed_label','contigviewtop' => 'gene_label','alignsliceviewbottom' => 'as_collapsed_label','cytoview' => 'gene_label'},'multi_caption' => 'Ensembl IG genes, or Merged Ensembl and Havana IG genes','key' => 'ensembl_IG_gene'}
345 ncRNA_pseudogene ncRNA pseudogenes imported from the manual annotation produced by Sean Eddy group. ncRNA pseudogene 1 {'colour_key' => 'rna_[status]','label_key' => '[text_label] [display_label]','default' => {'contigviewbottom' => 'transcript_label','contigviewtop' => 'gene_label','cytoview' => 'gene_label','MultiTop' => 'gene_label','MultiBottom' => 'collapsed_label','alignsliceviewbottom' => 'as_collapsed_label'}}
346 xrefcoordinatemapping xrefcoordinatemapping xrefcoordinatemapping 1
347 ppapepX Pristionchus pacificus proteins aligned by WU-BlastX PpapepX 1
348 ppapepP Pristionchus pacificus proteins aligned by WU-BlastP PpapepP 1
349 jappepP Caenorhabditis japonica proteins aligned by WU-BlastP JappepP 1 350 jappepX Caenorhabditis japonica proteins aligned by WU-BlastX JappepX 1
351 zfish_protein Zebrafish proteins from <a rel="external" href="http://uniprot.org">UniProtKB</a> are aligned to the genome using <a rel="external" href="http://genome.cshlp.org/cgi/content/abstract/14/5/988?maxtoshow=&HITS=10&hits=10&RESULTFORMAT=&andorexactfulltext=and&searchid=1&FIRSTINDEX=0&sortspec=relevance&volume=14&firstpage=988&resourcetype=HWCIT">GeneWise</a>. Zebrafish prot. 1
352 brepepP Caenorhabditis brenneri proteins aligned by WU-BlastP BrepepP 1
353 brepepX Caenorhabditis brenneri proteins aligned by WU-BlastX BrepepX 1
354 baboon_protein Baboon proteins from <a rel="external" href="http://www.ncbi.nlm.nih.gov/RefSeq/">NCBI RefSeq</a> and <a rel="external" href="http://uniprot.org">UniProtKB/TrEMBL</a> are aligned to the genome using <a rel="external" href="http://genome.cshlp.org/cgi/content/abstract/14/5/988?maxtoshow=&HITS=10&hits=10&RESULTFORMAT=&andorexactfulltext=and&searchid=1&FIRSTINDEX=0&sortspec=relevance&volume=14&firstpage=988&resourcetype=HWCIT">GeneWise</a>. Baboon prot. 1
355 baboon_cdna Baboon cDNAs from <a rel="external" href="http://www.ncbi.nlm.nih.gov/RefSeq/">NCBI RefSeq</a> and <a rel="external" href="http://www.ebi.ac.uk/embl/">EMBL</a> are aligned to the genome using <a rel="external" href="http://www.biomedcentral.com/1471-2105/6/31">Exonerate</a>. Baboon RefSeq/EMBL cDNA 1 {'default' => {'contigviewbottom' => 'stack'},'type' => 'cdna'}
#add new entries for core databases above, the following are for functional genomics
#500 Nessie Hidden Markov Model based predictions based on tiling array data Nessie (TilingHMM) 1
#501 HitList Custom hit list HitList 1
#502 SupervisedHMM Supervised Hidden Markov Model SupervisedHMM 1
#503 PHALANX_ProbeAlign Genomic alignments for PHALANX arrays PHALANX_ProbeAlign 1 {'type' => '_oligo', 'key' => 'array_chip', 'colourset' => 'feature', 'display' =>'off' }
#504 ILLUMINA_WG_ProbeTranscriptAlign Transcript alignments for ILLUMINA_WG arrays ILLUMINA_WG_ProbeTranscriptAlign 1 {'type' => '_oligo', 'key' => 'array_chip', 'colourset' => 'feature', 'display' =>'off' }
#505 cisRED cisRED motif search (www.cisred.org) cisRED 1 {'type' => 'regulatory_regions', 'name' => 'cisRED Motifs', 'colourset' => 'synteny', 'display' =>'off' }
#506 Parzen Solexa clusters Parzen 1
#507 RegulatoryRegion Union of focus features, features overlapping focus features, and features that are contained within those RegulatoryRegion 1 {'type' => 'fg_regulatory_features', 'name' => 'Reg. Feats', 'display' =>'off', 'depth' => 10, 'default' => {'contigviewbottom' => 'normal', 'generegview' => 'normal'} }
#508 CODELINK_ProbeAlign Genomic alignments for CODELINK arrays CODELINK_ProbeAlign 1 {'type' => '_oligo', 'key' => 'array_chip', 'colourset' => 'feature', 'display' =>'off' }
#509 AFFY_ST_ProbeTranscriptAlign Transcript alignments for AFFY_ST arrays AFFY_ST_ProbeTranscriptAlign 1 {'type' => '_oligo', 'key' => 'array_chip', 'colourset' => 'feature', 'display' =>'off' }
#510 Wiggle Solexa clusters from wiggle data Parzen 1
#511 AGILENT_ProbeTranscriptAlign Transcript alignments for AGILENT arrays AGILENT_ProbeTranscriptAlign 1 {'type' => '_oligo', 'key' => 'array_chip', 'colourset' => 'feature', 'display' =>'off' }
#512 LiftOver Remapping to new assembly performed by LiftOver LiftOver 1
#513 NestedMICA BioTIFFIN BioTIFFIN 1 { 'type' => 'regulatory_regions', 'key' => 'feature_set', 'name' => 'REDfly/BioTIFFIN','multi_caption' => 'External data','key' => 'miRanda','colourset' => 'synteny', 'display' =>'off' }
#514 SangerPCR Ratio generated by standard Sanger PCR array processing SangerPCR 1
#515 VSN_GLOG Generalised log transformation based on VSN variance stabilised scores VSN_GLOG 1 {'type' => 'histone_modifications', 'name' => 'Histone Modifications', 'display' => 'off', 'renderers' => {'off' => 'Off', 'tiling' => 'Normal'} }
#516 Nessie_NG_STD_2 Hidden Markov Model based predictions based on tiling array data HMM predictions based on tiling array data 1 {'type' => 'ctcf', 'name' => 'CTCF', 'display' => 'off', 'renderers' => {'off' => 'Off', 'tiling' => 'Normal'} }
#517 AFFY_ST_ProbeAlign Genomic alignments for AFFY_ST arrays AFFY_ST_ProbeAlign 1 {'type' => '_oligo', 'key' => 'array_chip', 'colourset' => 'feature', 'display' =>'off' }
#518 VendorMap Original mapping provided by Array Vendor Vendor mapping 1
#519 AFFY_UTR_ProbeTranscriptAlign Transcript alignments for AFFY_UTR arrays AFFY_UTR_ProbeTranscriptAlign 1 {'type' => '_oligo', 'key' => 'array_chip', 'colourset' => 'feature', 'display' =>'off' }
#520 AFFY_UTR_ProbeAlign Genomic alignments for AFFY_UTR arrays AFFY_UTR_ProbeAlign 1 {'type' => '_oligo', 'key' => 'array_chip', 'colourset' => 'feature', 'display' =>'off' }
#521 RawValue Raw value Raw value 1
#522 VISTA VISTA Enhancer Assay (http://enhancer.lbl.gov/) VISTA 1
#523 REDfly CRM REDfly CRMs REDfly CRM 1 { 'type' => 'regulatory_regions', 'key' => 'feature_set', 'name' => 'REDfly/BioTIFFIN', 'multi_caption' => 'External data','key' => 'miRanda','colourset' => 'synteny', 'display' =>'off' }
#524 miRanda miRanda microRNA target prediction (http://microrna.sanger.ac.uk/targets) miRanda 1 {'type' => 'regulatory_regions', 'key' => 'feature_set', 'name' => 'cisRED/miRanda/VISTA', 'multi_caption' => 'External data','key' => 'miRanda','colourset' => 'synteny', 'display' =>'off' }
#525 REDfly TFBS REDfly TFBSs REDfly TFBSs 1 { 'type' => 'regulatory_regions', 'key' => 'feature_set', 'name' => 'REDfly/BioTIFFIN', 'multi_caption' => 'External data','key' => 'miRanda','colourset' => 'synteny', 'display' =>'off' }
#526 Co-occurrence Overlap Co-occurrence of overlapping feature types Co-occurrence Overlap 1
#527 PHALANX_ProbeTranscriptAlign Transcript alignments for PHALANX arrays PHALANX_ProbeTranscriptAlign 1 {'type' => '_oligo', 'key' => 'array_chip', 'colourset' => 'feature', 'display' =>'off' }
#528 AGILENT_ProbeAlign Genomic alignments for AGILENT arrays AGILENT_ProbeAlign 1 {'type' => '_oligo', 'key' => 'array_chip', 'colourset' => 'feature', 'display' =>'off' }
#529 ILLUMINA_WG_ProbeAlign Genomic alignments for ILLUMINA_WG arrays ILLUMINA_WG_ProbeAlign 1 {'type' => '_oligo', 'key' => 'array_chip', 'colourset' => 'feature', 'display' =>'off' }
#530 T.Biweight Weighted mean standardisation using the one step Tukey Biweight algorithm Tukey Biweight 1
#531 WindowInterval Window Interval WindowInterval 1
#532 probe2transcript Microarray probes from manufacturers are aligned to the genome by Ensembl, if the probe sequences are provided. The mapping is a two-step procedure outlined <a href="/info/docs/microarray_probe_set_mapping.html">here</a>. Probe2Transcript Annotation 0
#533 LEIDEN_ProbeTranscriptAlign Transcript alignments for LEDIEN arrays LEIDEN_ProbeTranscriptAlign 1 {'type' => '_oligo', 'key' => 'array_chip', 'colourset' => 'feature', 'display' =>'off' }
#534 LEIDEN_ProbeAlign Genomic alignments for LEIDEN arrays LEIDEN_ProbeAlign 1 {'type' => '_oligo', 'key' => 'array_chip', 'colourset' => 'feature', 'display' =>'off' }
#535 CODELINK_ProbeTranscriptAlign Transcript alignments for CODELINK arrays CODELINK_ProbeTranscriptAlign 1 {'type' => '_oligo', 'key' => 'array_chip', 'colourset' => 'feature', 'display' =>'off' }
#536 WormBaseExpressionXrefs Imported Wormbase microarray annotations WormBase Expression Xrefs 0