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Example Data Points

This release of Cavia porcellus data is assembled into scaffolds, so there are no chromosomes available to browse.

A few example data points :

• GeneScaffold: GeneScaffold_1128
• Gene: ENSCPOG00000000580
• Protein: ENSCPOP00000000491

About the Cavia porcellus genome

Assembly

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.

Annotation

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.

• Details of the gene-scaffold construction and subsequent gene-build

Mammalian Genome Project

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.

What's New in Ensembl 50

Cavia porcellus News

• Non-coding genes
  These have been updated for most species, including an miRNA update and HGNC names where possible.
• Multiple alignments
  

  The multiple alignments are being extended with new species and 2X genomes.
  Read more...

General News

• Canonical Transcripts
  

  Canonical transcripts have been defined for all genes in the core databases.
  Read more...

• SSAHA
  From release 50 we will no longer be providing SSAHA sequence search. If you wish to run your own SSAHA sequence search you can download the files to generate the search hashes from our FTP site.
• Projections of gene names and GO terms
  These have been done as usual, between a variety of species.

More news...

Statistics

How the statistics are calculated