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Commit a06e37bf authored by Steve Trevanion's avatar Steve Trevanion
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names for merged tracke ni multiviews

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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 {'colour_key' => '[biotype]_[status]','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'},'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'}
......@@ -81,9 +81,9 @@
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'},'key' => 'ensembl'}
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'},'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. Vega 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'},'key' => 'ensembl'}
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. Vega 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'},'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
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
......@@ -105,7 +105,7 @@
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'},'key' => 'ensembl'}
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'},'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&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
......@@ -248,7 +248,7 @@
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'},'key' => 'ensembl'}
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'},'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]'}
......@@ -341,8 +341,8 @@
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=&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]','label_key' => '[text_label] [display_label]','default' => {'contigviewbottom' => 'transcript_label','contigviewtop' => 'gene_label','cytoview' => 'gene_label'}}
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. Vega gene 1 {'colour_key' => '[biotype]_[status]','caption' => 'Ensembl/Havana gene','label_key' => '[text_label] [display_label]','name' => 'Merged Ensembl and Havana Genes','default' => {'contigviewbottom' => 'transcript_label','contigviewtop' => 'gene_label','cytoview' => 'gene_label'},'key' => 'ensembl'}
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 gene','label_key' => '[text_label] [display_label]','default' => {'contigviewbottom' => 'transcript_label','contigviewtop' => 'gene_label','cytoview' => 'gene_label'},'key' => 'ensembl','multi_caption' => 'Ensembl genes, or Merged Ensembl and Havana genes'}
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. Vega gene 1 {'colour_key' => '[biotype]_[status]','caption' => 'Ensembl/Havana gene','label_key' => '[text_label] [display_label]','name' => 'Merged Ensembl and Havana Genes','default' => {'contigviewbottom' => 'transcript_label','contigviewtop' => 'gene_label','cytoview' => 'gene_label'},'key' => 'ensembl','multi_caption' => 'Ensembl genes, or Merged Ensembl and Havana genes'}
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'}}
346 xrefcoordinatemapping xrefcoordinatemapping xrefcoordinatemapping 1
347 ppapepX Pristionchus pacificus proteins aligned by WU-BlastX PpapepX 1
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