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Commit 03471416 authored by Steve Trevanion's avatar Steve Trevanion
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minor tweaks

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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 {'label_key' => '[text_label] [display_label]','default' => {'contigviewbottom' => 'transcript_label','contigviewtop' => 'gene_label','cytoview' => 'gene_label'}}
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'}}
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'}
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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/viewcvs.cgi/">Sanger Centre 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]','label' => '[text_label] [display_label]'}
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'}}
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
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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]'}
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, Fgenes). 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]"}
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, Fgenes). 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'}}
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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/viewcvs.cgi/">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">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]"}
147 otter_external See <a href="http://vega.sanger.ac.uk/info/about/man_annotation.html">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://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>. Medaka RefSeq/EMBL cDNA 1 {'default' => {'contigviewbottom' => 'stack'},'type' => 'cdna'}
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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=&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 UniProt prot. 1
203 singapore_protein Protein-based gene-prediction Singapore gene 1 {'label' => '[text_label] [display_label]'}
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'}}
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'}}
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
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