Commit fe10aae9 authored by Beth Yates's avatar Beth Yates
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changed RFAM link at Giulietta's request - bp1

parent 642ee7d0
......@@ -120,7 +120,7 @@
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=&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>. 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=&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>. Macaque UniProt prot. 1
120 ncRNA Non-coding RNA (ncRNA) is predicted using sequences from <a href="http://www.sanger.ac.uk/Software/Rfam/index.shtml">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'}}
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'}}
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]'}
......@@ -138,7 +138,7 @@
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'}}
138 RfamBlast <a href="/info/docs/genebuild/ncrna.html" class="cp-external">Positions</a>Positions of ncRNAs (non-coding RNAs) from the <a rel="external" href="http://www.sanger.ac.uk/Software/Rfam/">Rfam </a> database are shown. Initial BLASTN hits of genomic sequence to RFAM ncRNAs are clustered and filtered by E value. These hits are supporting evidence for ncRNA genes. RFAM ncRNA gene 1 {'type'=>'rna'}
138 RfamBlast <a href="/info/docs/genebuild/ncrna.html" class="cp-external">Positions</a>Positions of ncRNAs (non-coding RNAs) from the <a rel="external" href="http://rfam.sanger.ac.uk/">Rfam </a> database are shown. Initial BLASTN hits of genomic sequence to RFAM ncRNAs are clustered and filtered by E value. These hits are supporting evidence for ncRNA genes. RFAM ncRNA gene 1 {'type'=>'rna'}
139 orangutan_protein Orangutan proteins from Swiss-Prot/TrEMBL aligned to the genome using GeneWise (E. Birney et al., Genome Res. 2004 14:988-95) Orangutan prot. 1
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
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