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Commit b4430758 authored by Steve Trevanion's avatar Steve Trevanion
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couple of typos, plus new worm entries

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71 human_est Homo sapiens '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>. Human EST 1 {'type'=>'est'}
72 cow_protein Cow 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=&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>. Cow prot. 1
73 caenorhabditis_est Caenorhabditis ESTs aligned to the genome using BLAT (excluding C.elegans) caenorhabditis EST 1 {'type'=>'est'}
74 singapore_est Expressed Sequence Tag (EST)-based gene prediction provided by B. Kumarasamy and E. Stupka. Singapore gene 1 {'label_key' => '[text_label] [display_label]','key' => 'singapore_est'}
74 singapore_est Expressed Sequence Tag (EST)-based gene prediction provided by B. Kumarasamy and E. Stupka. Singapore gene 1 {'label_key' => '[text_label] [display_label]','key' => 'singapore_est'}
75 Uniprot_SW Proteins from the <a rel="external" href="http://uniprot.org">UniProtKB Swiss-Prot</a> database, aligned to the genome. UniProt prot. 1
76 drosophila_est Drosophila melanogaster '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>. Fly EST 1 {'type'=>'est'}
77 Uniprot_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 UniProt prot. 1
......@@ -123,7 +123,7 @@
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'}}
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]','label' => '[text_label] [display_label]', 'multi_key' => 'estgene'}
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]', 'multi_key' => 'estgene'}
124 human_refseq Human proteins from <a rel="external" href="http://www.ncbi.nlm.nih.gov/RefSeq/">NCBI RefSeq</a> used in the <a href="/info/docs/genebuild/index.html" class="cp-external">genebuild</a> are aligned to the genome using <a rel="external" href="http://genome.cshlp.org/cgi/content/abstract/14/5/988?maxtoshow=&amp;HITS=10&amp;hits=10&amp;RESULTFORMAT=&amp;andorexactfulltext=and&amp;searchid=1&amp;FIRSTINDEX=0&amp;sortspec=relevance&amp;volume=14&amp;firstpage=988&amp;resourcetype=HWCIT">GeneWise</a>. Human RefSeq prot. 1
125 Vertrna Positions of vertebrate mRNAs along the genome. mRNAs are from the <a rel="external" href="http://www.ebi.ac.uk/embl/">EMBL</a> database. Initial alignments are performed using TBLASTN of Genscan-predicted peptides against EMBL mRNAs. EMBL vertebrate cDNA 1 {'type' => 'cdna','default' => {'contigviewbottom'=>'stack'}}
126 fugu_cdna Takifugu cDNAs from <a rel="external" href="http://www.ebi.ac.uk/embl/">EMBL</a> and <a rel="external" href="http://www.ncbi.nlm.nih.gov/Genbank/">Genbank</a> are aligned to the genome using <a rel="external" href="http://www.biomedcentral.com/1471-2105/6/31">Exonerate</a>. Takifugu cDNA 1 {'default' => {'contigviewbottom' => 'stack'},'type' => 'cdna'}
......@@ -202,7 +202,7 @@
200 slimswissprotX Swissprot proteins aligned by WU-BlastX slimswissprotX 1
201 aberration_junction Feature imported from <a rel="external" href="http://www.flybase.org">FlyBase</a>. Aberration junction 1
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]','key' => 'singapore_est'}
203 singapore_protein Protein-based gene-prediction Singapore gene 1 {'label' => '[text_label] [display_label]','key' => 'singapore_est'}
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
......@@ -350,3 +350,5 @@
349 jappepP Caenorhabditis japonica proteins aligned by WU-BlastP JappepP 1
350 jappepX Caenorhabditis japonica proteins aligned by WU-BlastX JappepX 1
351 zfish_protein Zebrafish 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>. Zebrafish prot. 1
352 brepepP Caenorhabditis brenneri proteins aligned by WU-BlastP BrepepP 1
353 brepepX Caenorhabditis brenneri proteins aligned by WU-BlastX BrepepX 1
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