Ensembl X.tropicalis

Example Data Points

This release of X.tropicalis 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:

• Scaffold: Scaffold_1
• Scaffold: Scaffold_20
• Scaffold: Scaffold_40

About the X. tropicalis genome

Assembly

The Xenopus tropicalis genome assembly version 4.1 [August 2005] is the fourth of a series of preliminary assembly releases by the JGI that are planned as part of the ongoing X. tropicalis genome project. This Ensembl website presents the sequence data provided by the JGI.

The reads were assembled using JAZZ, the JGI assembler, producing a genome of approximately 1.5 Gb. The assembly contains 19,501 scaffolds with an average coverage of 7.65X. Roughly half of the genome is contained in 272 scaffolds, all at least 1.56 Mb in length. In this update to the 4.0 assembly, some scaffolds showing homology to a known prokaryotic contaminant as well as non-cellular or vector contamination have been removed - see the JGI website (above) for more information.

Annotation

The gene set for Xenopus tropicalis was built using a modified version of the standard Ensembl pipeline. Both Xenopus tropicalis and Xenopus laevis proteins were used to predict gene structures. cDNAs from both species were used to add UTRs. Gene predictions were also based on Xenopus tropicalis cDNAs manually annotated in the July 2005 jamboree. Finally, gene predictions based on UniProt proteins were used to fill gaps in the annotation.

What's New in Ensembl 43

Xenopus tropicalis News

There is no Xenopus tropicalis-specific news this release.

General News

• A faster ContigView
  ContigView now displays information faster. Each open panel in ContigView is prepared in parallel, and then returned to the page when complete. This results in faster page loads.
• New - Table view
  In ContigView you can now click on the name of a feature alignment track and select 'DAS Table View' (or for DAS tracks 'view DAS reponse') from the zmenu.
  Read more...
• New search option
  It is now possible to select whether to search either the Ensembl website or the EBI site when using Ensembl search.
• Changes to Xrefs
  The following changes have been made to xrefs for Release 43:
  • We have made improvements to EntrezGene xrefs, to allow for better handling of names and synonyms
  • Incorporation of new Illumina probe data as xrefs.
    Read more...
  • API changes to ensembl-functgenomics
    A new DataSet API has been developed aimed at making web display much easier.

  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