Ensembl C.savignyi

Example Data Points

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

A few example data points :

• Transcript: SNAP00000081384
• Region: reftig_35:1-16756
• Region: reftig_2291

About the C.savignyi genome

Assembly

The genome of a single Ciona savignyi from San Francisco Bay was shotgun-sequenced by the Broad Institute and assembled using Arachne2. The Sidow lab at Stanford used this as a basis for the assembly [details].

The assembly consists of 374 Reftigs, totalling 174 Megabases, with a Contig N50 of 141Kb and Reftig N50 size of 1800Kb.

Annotation

The standard Ensembl mammalian pipeline was modified for annotation of the Ciona savignyi genome, owing to the lack of genomic information from closely-related species. Thus, in addition to aligning known Ciona proteins to the sequence (as per the standard pipeline), we aligned Ciona-specific cDNA and EST sequences against the genome, and then used these in conjunction with protein data from other species to build additional gene models.

What's New in Ensembl 39

Ciona savignyi News

• New Ciona savignyi assembly and genebuild
  The Ciona savignyi assembly 2.0, previously available on pre.ensembl.org, now has a completed Ensembl genebuild.
  Read more...

General News

• Bug fixes
  In order to fix some problems with the store() method in Gene and Transcript, DBEntryAdaptor and AttributeAdaptor now require a gene/transcript/translation dbID rather than object as one of their arguments (please see POD for details).
• Multiple versions of genes
  The schema and API have been changed to allow multiple versions of genes, transcripts and exons, for better integration with Otter (the Ensembl-based database schema used as a backend for Havana).
  Read more...
• New MLAGAN groups
  A new 3-way MLAGAN Primate group has been created, containing Human, Chimp and macaque.
  Read more...
• Compara - whole genome alignments, syntenies and families
  

  Whome Genome Alignments.
  Read more...

More news...

Statistics