From df6159cf694bf2d111efd3c53fb0b5983d353f80 Mon Sep 17 00:00:00 2001
From: Steve Trevanion <st3@sanger.ac.uk>
Date: Mon, 14 Sep 2009 15:05:12 +0000
Subject: [PATCH] changed default renderers for mcv and asv
---
.../analysis.descriptions | 46 +++++++++----------
1 file changed, 23 insertions(+), 23 deletions(-)
diff --git a/misc-scripts/analysis_description/analysis.descriptions b/misc-scripts/analysis_description/analysis.descriptions
index c1c95ba835..cd769a7f08 100644
--- a/misc-scripts/analysis_description/analysis.descriptions
+++ b/misc-scripts/analysis_description/analysis.descriptions
@@ -18,7 +18,7 @@
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' => 'transcript_label','alignsliceviewbottom' => 'transcript_label'},'multi_caption' => 'Ensembl genes, or Merged Ensembl and Havana genes'}
+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'}
@@ -30,13 +30,13 @@
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' => 'transcript_label','contigviewtop' => 'gene_label','alignsliceviewbottom' => 'transcript_label','cytoview' => 'gene_label'}, 'key' => 'ensembl', 'name' => 'Ensembl gene', 'multi_caption' => 'Ensembl genes, or Merged Ensembl and Havana genes'}
+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' => 'transcript_label','alignsliceviewbottom' => 'transcript_label'},'key' => 'ncRNA'}
+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'}
@@ -49,10 +49,10 @@
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' => 'transcript_label','alignsliceviewbottom' => 'transcript_label'}}
+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' => 'transcript_label','alignsliceviewbottom' => 'transcript_label'},'key' => 'wormbase'}
+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'}}
@@ -81,19 +81,19 @@
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' => 'transcript_label','alignsliceviewbottom' => 'transcript_label'},'key' => 'ensembl','multi_caption' => 'Ensembl genes, or Merged Ensembl and Havana genes'}
+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. 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','MultiTop' => 'gene_label','MultiBottom' => 'transcript_label','alignsliceviewbottom' => 'transcript_label'},'key' => 'ensembl','multi_caption' => 'Ensembl genes, or Merged Ensembl and Havana genes'}
+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','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' => 'transcript_label','alignsliceviewbottom' => 'transcript_label'},'key' => 'ncRNA'}
+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' => 'transcript_label','alignsliceviewbottom' => 'transcript_label'},'key' => 'ncRNA'}
+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'}
@@ -105,22 +105,22 @@
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' => 'transcript_label','alignsliceviewbottom' => 'transcript_label'},'key' => 'ensembl','multi_caption' => 'Ensembl genes, or Merged Ensembl and Havana genes'}
+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' => 'transcript_label','alignsliceviewbottom' => 'transcript_label'}}
+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' => 'transcript_label','alignsliceviewbottom' => 'transcript_label'}}
+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' => 'transcript_label','alignsliceviewbottom' => 'transcript_label'}}
+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'}
@@ -143,7 +143,7 @@
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' => 'transcript_label','alignsliceviewbottom' => 'transcript_label'},'key' => 'ncRNA'}
+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
@@ -172,7 +172,7 @@
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' => 'transcript_label','alignsliceviewbottom' => 'transcript_label'}}
+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
@@ -183,13 +183,13 @@
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' => 'transcript_label','alignsliceviewbottom' => 'transcript_label'},'key' => 'ncRNA'}
+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' => 'transcript_label','alignsliceviewbottom' => 'transcript_label'}}
+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
@@ -206,7 +206,7 @@
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' => 'transcript_label','alignsliceviewbottom' => 'transcript_label'}}
+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
@@ -221,7 +221,7 @@
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' => 'transcript_label','contigviewtop' => 'gene_label','alignsliceviewbottom' => 'transcript_label','cytoview' => 'gene_label'},'multi_caption' => 'Ensembl IG genes, or Merged Ensembl and Havana IG genes','key' => 'ensembl_IG_gene'}
+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'}
@@ -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','MultiTop' => 'gene_label','MultiBottom' => 'transcript_label','alignsliceviewbottom' => 'transcript_label'},'key' => 'ensembl','multi_caption' => 'Ensembl genes, or Merged Ensembl and Havana genes'}
+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]'}
@@ -341,9 +341,9 @@
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' => 'transcript_label','contigviewtop' => 'gene_label','alignsliceviewbottom' => 'transcript_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. Vega 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' => 'transcript_label','contigviewtop' => 'gene_label','alignsliceviewbottom' => 'transcript_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' => 'transcript_label','alignsliceviewbottom' => 'transcript_label'}}
+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. Vega 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
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