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Commit e187461c authored by Amonida Zadissa's avatar Amonida Zadissa
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Removed duplicated entries.

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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=&amp;HITS=10&amp;hits=10&amp;RESULTFORMAT=1&amp;author1=Bateman&amp;andorexacttitle=and&amp;andorexacttitleabs=and&amp;andorexactfulltext=and&amp;searchid=1&amp;FIRSTINDEX=0&amp;sortspec=relevance&amp;resourcetype=HWCIT">Pfam</a> database. Pfam domain 1 {'type'=>'domain'}
85 PercentGC Percentage of G/C bases in the sequence. GC content 1
......@@ -125,11 +124,9 @@
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=&amp;HITS=10&amp;hits=10&amp;RESULTFORMAT=&amp;andorexactfulltext=and&amp;searchid=1&amp;FIRSTINDEX=0&amp;sortspec=relevance&amp;volume=14&amp;firstpage=988&amp;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=&amp;HITS=10&amp;hits=10&amp;RESULTFORMAT=1&amp;author1=Haft&amp;andorexacttitle=and&amp;andorexacttitleabs=and&amp;andorexactfulltext=and&amp;searchid=1&amp;FIRSTINDEX=0&amp;sortspec=relevance&amp;fdate=1/1/2003&amp;tdate=12/31/2003&amp;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&amp;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=&amp;HITS=10&amp;hits=10&amp;RESULTFORMAT=&amp;andorexactfulltext=and&amp;searchid=1&amp;FIRSTINDEX=0&amp;sortspec=relevance&amp;volume=14&amp;firstpage=988&amp;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]'}
......@@ -210,7 +207,6 @@
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&amp;_udi=B6WK7-457D7V9-K&amp;_user=776054&amp;_rdoc=1&amp;_fmt=&amp;_orig=search&amp;_sort=d&amp;view=c&amp;_version=1&amp;_urlVersion=0&amp;_userid=776054&amp;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
......@@ -234,11 +230,9 @@
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&amp;_udi=B6WK7-45VGF7T-9&amp;_user=776054&amp;_rdoc=1&amp;_fmt=&amp;_orig=search&amp;_sort=d&amp;view=c&amp;_version=1&amp;_urlVersion=0&amp;_userid=776054&amp;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=&amp;HITS=10&amp;hits=10&amp;RESULTFORMAT=&amp;andorexactfulltext=and&amp;searchid=1&amp;FIRSTINDEX=0&amp;sortspec=relevance&amp;volume=14&amp;firstpage=988&amp;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
......@@ -252,14 +246,11 @@
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=&amp;HITS=10&amp;hits=10&amp;RESULTFORMAT=&amp;andorexactfulltext=and&amp;searchid=1&amp;FIRSTINDEX=0&amp;sortspec=relevance&amp;volume=14&amp;firstpage=988&amp;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&amp;rendertype=abstract">Cluster-Merge algorithm</a>. EST-based gene 1 {'label' => '[text_label] [display_label]'}
......@@ -293,7 +284,6 @@
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
......@@ -343,7 +333,6 @@
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=&amp;HITS=10&amp;hits=10&amp;RESULTFORMAT=1&amp;author1=Lefranc&amp;andorexacttitle=and&amp;andorexacttitleabs=and&amp;andorexactfulltext=and&amp;searchid=1&amp;FIRSTINDEX=0&amp;sortspec=relevance&amp;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
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