Ensembl Guinea Pig

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 44

Cavia porcellus News

• Patch for Ensembl Guineapig database
  Ensembl Cavia porcellus has been patched to fix the stable ID problems in release 43.

General News

• ncRNAs for Ensembl chordates
  All Ensembl genebuild databases (i.e. excluding the imported invertebrate databases for mosquitoes, fruit fly, worm and yeast) have been updated with new ncRNA data.
• Compara updates
  

  Pairwise alignments

  • Platypus (Ornithorhynchus anatinus) OANA5 BLASTZ_NET vs Mus musculus (NCBIM36)
  • Cat (Felis catus) BLASTZ_NET vs Canis familiaris (BROADD2)
  • Treeshrew (Tupaia belangeri) BLASTZ_NET vs Homo sapiens (NCBI36)
  • Hedgehog (Erinaceus europaeus) BLASTZ_NET vs Homo sapiens (NCBI36)
  • Opossum (Monodelphis domestica) BROAD5 (new assembly) BLASTZ_NET vs Homo sapiens (NCBI36)
  • Bushbaby (Otolemur garnetti) (2X genome, new species) BLASTZ_NET vs Homo sapiens (NCBI36)
  • Ground squirrel (Spermophilus tridecemlineatus) (2X genome, new species) BLASTZ_NET vs Homo sapiens (NCBI36)
  • Little brown bat (Myotis lucifugus) (2X genome, new species) BLASTZ_NET vs Homo sapiens (NCBI36)

  Multiple alignments

  PECAN (vertebrates) 10 ways.
  Read more...

• Schema changes
  There have been no major schema changes this release, however we are starting to systematically work through the schema to make sure that all column types are appropriate for the data they are likely to hold.
  Read more...
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More news...

Statistics

* Total number of base pairs = sum of lengths of DNA table

** Reference assembly (Golden path) length = sum of non-redundant top level seq regions