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Commit 5d1ce6c9 authored by Daniel Rios's avatar Daniel Rios
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file updated with some tweaks

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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'}
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'}
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/viewcvs.cgi/">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'}
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
......@@ -303,9 +303,9 @@
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=&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>. 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
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 Anopheles 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'}
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
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