This release of Cavia porcellus data is assembled into scaffolds, so there are no chromosomes available to browse.
A few example data points :
This is the first release of the low-coverage 1.92X assembly of the
Guinea Pig (Cavia porcellus). The genome sequencing
and assembly is provided by the
Broad Institute.
The N50 size is the length such that 50% of the assembled genome lies in blocks of the N50 size or longer. The N50 length for supercontigs is 14.57 kb and is 2.80 kb for contigs. The total number of bases in supercontigs is 3.37 Gb and in contigs is 1.95 Gb.
Owing to the fragmentary nature of this preliminary assembly, it was necessary to arrange some scaffolds into "gene-scaffold" super-structures,in order to present complete genes. There are 8,008 such gene scaffolds, with identifiers of the form "GeneScaffold_1".
In addition to the projection based genebuild, genewise was used to align Cavia porcellus proteins to the genome, including the gene-scaffolds and Cavia porcellus cDNAs and ESTs were aligned using exonerate.
Cavia porcellus is one of 16 mammals that will be sequenced as part of the Mammalian Genome Project, funded by the National Institutes of Health (NIH). A group of species were chosen to maximise the branch length of the evolutionary tree while representing the diversity of mammalian species. Low-coverage 2X assemblies will be produced for these mammals and used in alignments for cross-species comparison. The aim is to increase our understanding of functional elements, especially in the human genome.
There is no Cavia porcellus-specific news this release.
Only minor changes to the database schema this release:
| Assembly: | cavPor2, Jun 2006 |
| Genebuild: | Ensembl, Oct 2006 |
| Database version: | 44.1a |
| Known genes: | 202 |
| Novel genes: | 13,862 |
| Pseudogenes: | 1,703 |
| RNA genes: | 1,749 |
| Genscan gene predictions: | 90,863 |
| Gene exons: | 208,125 |
| Gene transcripts: | 15,922 |
| Base Pairs*: | 1,949,659,178 |
| Golden Path Length**: | 3,414,840,009 |
* Total number of base pairs = sum of lengths of DNA table
** Reference assembly (Golden path) length = sum of non-redundant top level seq regions
© 2008 WTSI / EBI. Ensembl is available to download for public use - please see the code licence for details.
