Commit 44443bd0 authored by Steve Trevanion's avatar Steve Trevanion
Browse files

updated web_data for BACends, added FOSends

parent 1ec56716
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1 ARRAY_LIV_GAMDETOX_0.25k_v1 Vectorbase probe alignments: LIV_GAMDETOX_0.25k_v1 OLIGO LIV_GAMDETOX_0.25k_v1 1
2 VirginiaTech_Insect_TE Transposable elements (TE) catalogued by Jake Tu, Virginia Tech VirginiaTech Insect TE 1
3 BACends Bacterial Artificial Chromosome (end sequences) of library clones that were used in the sequencing project are aligned to the genome using <a rel="external" href="http://www.sanger.ac.uk/Software/analysis/SSAHA2/">SSAHA2</a>. BAC ends 1 {'default' => {'contigviewbottom' => 'gene_label','contigviewtop' => 'gene_label','cytoview' => 'gene_label'}}
3 BACends Bacterial Artificial Chromosome (end sequences) of library clones that were used in the sequencing project are aligned to the genome using <a rel="external" href="http://www.sanger.ac.uk/Software/analysis/SSAHA2/">SSAHA2</a>. BAC ends 1 {'default' => {'contigviewbottom' => 'gene_label','contigviewtop' => 'gene_label','cytoview' => 'gene_label'}, 'show_strands' => '1'}
4 BlastmiRNA Positions of miRNAs along the genome are shown. A BLASTN of genomic sequence regions against <a rel="external" href="http://microrna.sanger.ac.uk">miRBase</a> sequences is performed, and hits are clustered and filtered by E value. Aligned genomic sequence is then checked for possible secondary structure using RNAFold. If evidence is found that the genomic sequence could form a stable hairpin structure the locus is used to create a miRNA gene model. The resulting BLAST hit is used as supporting evidence for the miRNA gene. See <a href="/info/docs/genebuild/ncrna.html" class="cp-external">article</a>. miRBase miRNA 1 {'type'=>'rna'}
5 other_protein For various species, proteins from <a rel="external" href="http://uniprot.org">UniProtKB</a> are aligned to the genome with <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>. Other sp. prot. 1
6 cint_cdna Ciona intestinalis cDNA sequences from 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 cDNA 1 {'default' => {'contigviewbottom' => 'stack'},'type' => 'cdna'}
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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
330 FOSends End sequences of Fosmid library clones used in the sequencing project aligned to the genome using <a rel="external" href="http://www.sanger.ac.uk/Software/analysis/SSAHA2/">SSAHA2</a>. FOS ends 1 {'default' => {'contigviewbottom' => 'gene_label','contigviewtop' => 'gene_label','cytoview' => 'gene_label'}, 'show_strands' => '1'}
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