The compara orthology build has been updated to include the new Opossum genome, and chimp dnafrag names have been changed to take account of the re-numbering of the Chimp chromosomes (see Chimp news for more information).
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All variation databases now include the new consequence_type 'REGULATORY_REGION'.
Features which have accompanying Gene locations, e.g. some AffyProbes, now display a table of gene names and descriptions at the top of the view page. See an example....
The Chimp chromosome numbers have been changed to the new primate standard proposed by E.H.
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This release of Cow data is assembled into scaffolds, so there are no chromosomes available to browse. Use the BLAST and SSAHA buttons in the menu bar, left, to locate data.
A few example data points:
Btau_1.0 is a preliminary 3x assembly of the draft genome sequence of cow (Bos taurus), Hereford breed, using whole genome shotgun (WGS) reads from small insert clones. The project coordination and genome sequencing and assembly is provided by the Human Genome Sequencing Center at Baylor College of Medicine.
The N50 size is the length such that 50% of the assembled genome lies in blocks of the N50 size or longer. The N50 of the contigs is 4.2 kb. The N50 of the scaffolds is 13.5 kb. The total length of all contigs is 2.26 Gb. When the gaps between contigs in scaffolds are included, the total span of the assembly is 2.34 Gb.
The fragmentary nature of this preliminary assembly leads to single gene structures being distributed across many scaffolds. In order to present as-far-as-possible complete gene structures, it was therefore necessary to assemble some scaffolds into "gene-scaffold" super-structures. There are 10075 such gene-scaffolds, with identifiers of the form "GeneScaffold_1".
The standard Ensembl gene-build pipeline is unsuitable for low-coverage, fragmentary genomes such as this. It has therefore been necessary to devleop a new method that utilises a whole genome alignment (WGA) to an annotated, reference genome (in this case, Homo_sapiens). Cow gene structures have been derived largely by projecting human gene-structures through the WGA onto the cow sequence.
Full details of the gene-scaffold construction and subsequent gene-build...
| Assembly: | Btau 1.0, Sep 2004 |
| Genebuild: | Ensembl, July 2005 |
| Database version: | 35.1 |
| Gene predictions : | 22,013 |
| Genscan gene predictions: | 103,597 |
| Gene exons: | 239,889 |
| Gene transcripts: | 29,363 |
| Base Pairs: | 565,382,643 |
| Golden Path Length: | 2,259,526,392 |
| Most common InterPro domains: | Top 40 Top 500 |
© 2008 WTSI / EBI. Ensembl is available to download for public use - please see the code licence for details.
