131 scanprosite Protein domains and motifs from the <a rel="external" href="http://www.ebi.ac.uk/ppsearch/">PROSITE</a> profiles database are aligned to the genome. PROSITE patterns 1 {'type'=>'domain'}
132 stickleback_protein Gasterosteus aculeatus 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>. Stickleback prot. 1
133 Medaka_Genome_Project Genes predicted by the Medaka Genome Project, viz. the University of Tokyo (http://medaka.utgenome.org/) and the National Institute of Genetics (http:// dolphin.lab.nig.ac.jp/medaka/). MGP gene 1 {'label_key' => '[text_label] [display_label]','label' => '[text_label] [display_label]'}
134 otter Finished genomic sequence is analysed on a clone by clone basis using a combination of similarity searches against DNA and protein databases as well as a series of ab initio gene predictions (GENSCAN, Fgenes). In addition, comparative analysis using vertebrate datasets is used to aid novel gene discovery. The data gathered in these steps is then used to manually annotate the clone adding gene structures, descriptions and poly-A features. The annotation is based on supporting evidence only. Vega Havana gene 1 {'colour_key'=>'[gene.logic_name]_[gene.biotype]'}
134 otter Finished genomic sequence is analysed on a clone by clone basis using a combination of similarity searches against DNA and protein databases as well as a series of ab initio gene predictions (GENSCAN, Augustus). In addition, comparative analysis using vertebrate datasets is used to aid novel gene discovery. The data gathered in these steps is then used to manually annotate the clone adding gene structures, descriptions and poly-A features. The annotation is based on supporting evidence only. Vega Havana gene 1 {'colour_key'=>'[gene.logic_name]_[gene.biotype]'}
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'}}
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313 refseq_mouse Murine cDNAs from <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>. Mouse RefSeq cDNA 1 {'default' => {'contigviewbottom' => 'stack'},'type' => 'cdna'}
314 refseq_human Human cDNAs from <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>. Human RefSeq cDNA 1 {'default' => {'contigviewbottom' => 'stack'},'type' => 'cdna'}
315 refseq_zebrafish Zebrafish cDNAs from <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>. Zebrafish RefSeq cDNA 1 {'default' => {'contigviewbottom' => 'stack'},'type' => 'cdna'}
316 augustus Ab initio prediction of protein coding genes by Augustus, a software tool for gene prediction in eukaryotes based on a Generalized Hidden Markov Model. Stanke et al., Nucleic Acids Res., 34: W435-W439 (2006). Augustus 1
316 augustus Ab initio prediction of protein coding genes by Augustus, a software tool for gene prediction in eukaryotes based on a Generalized Hidden Markov Model. Stanke et al., Nucleic Acids Res., 34: W435-W439 (2006). Augustus prediction 1
317 RepeatMasker 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
318 polyA_signal PolyA signals identified during manual annotation PolyA Signal 1
319 pseudo_polyA Poly A like structures associated with pseudogenes Pseudo PolyA 1
320 RSS The IG and T-cell recombination signal sequences motifs are canonically considered to be nonamers and heptamers seperated by spacers of 12 or 23 nucleotides and are found at the 3' end of the V elements, the 5' end of the J elements, and on both sides of the D elements [ V(D)J recombination mechanism]. RSS Motif. 1
321 otter_eucomm Virtual mouse genes, produced for the <a rel="external" href="http://www.eucomm.org">/EUCOMM</a> project, representing the gene structure produced after knockout of exons critical to gene function. KO genes (EUCOMM) 1
322 otter_komp Virtual mouse genes, produced for the <a rel="external" href="http://www.nih.gov/science/models/mouse/knockout/">/KOMP</a> project, representing the gene structure produced after knockout of exons critical to gene function. KO genes (KOMP) 1
321 otter_eucomm Virtual mouse genes, produced for the <a rel="external" href="http://www.eucomm.org">/EUCOMM</a> project, representing the gene structure produced after knockout of exons critical to gene function. KO gene (EUCOMM) 1 {'colour_key' => '[gene.logic_name]_[gene.biotype]'}
322 otter_komp Virtual mouse genes, produced for the <a rel="external" href="http://www.nih.gov/science/models/mouse/knockout/">/KOMP</a> project, representing the gene structure produced after knockout of exons critical to gene function. KO gene (KOMP) 1 {'colour_key' => '[gene.logic_name]_[gene.biotype]'}
323 EUCOMM This mouse track is linked to the mouse Knockout gene track. It shows the locations of exons identified by Havana as being critical for correct translation of the longest transcript at a specific loci. Knockout Deletion 1
324 est2genome_fish Alignment of 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> Zebrafish EST (EST2genome) 1 {'type'=>'est'}
325 PCodDensity Density of Vega protein coding genes Genes (density) 1
326 PTransDensity Density of Vega processed transcripts Genes (density) 1
327 PseudoGeneDensity Density of Vega pseudogenes Genes (density) 1
328 IGGeneDensity Density of Vega IG genes Genes (density) 1
329 TECGeneDensity Density of Vega TEC genes Genes (density) 1
