Release VB_2011-02

Note, this is legacy information that refers to an older version of the VectorBase website.
Hyperlinks have been removed and URLs may no longer be valid.

Overview

Highlights of the February release of VectorBase (VB-2011-02) include:

  • Pre-site for Rhodnius prolixus. Facilitates the browsing of the genome assembly with repeats, ESTs, RNA-seq and proteins alignments. GenScan ab-initio predictions as well as EST-build genes are presented.
    Please note that these gene predictions are "work in progress" and will not be maintained as such in the final gene set. Full gene predictions will follow in a subsequent VectorBase release.
  • Rhodnius prolixus assembly available for BLAST searching.
  • Improved access to Anopheline RNAseq datasets via BLAST (see Tools below).
  • New database cross-reference sources for Anopheles gambiae and Aedes aegypti including AnoXcel data and PubMed references.

Genomes

Fully released genomes, with gene predictions

Species Assembly Gene set GenBank WGS
Aedes aegypti Liverpool AaegL1 AaegL1.2 AAGE02000000
Anopheles gambiae PEST AgamP3 AgamP3.6 AAAB01000000
Culex quinquefasciatus JHB CpipJ1 CpipJ1.2 AAWU01000000
Ixodes scapularis Wikel IscaW1 IscaW1.1 ABJB01000000
Pediculus humanus USDA PhumU1 PhumU1.2 AAZO01000000

Pre-released genomes, with mapped data but no gene predictions

Species Assembly GenBank WGS Data available
Anopheles gambiae M AgamM1 ABKP00000000 Repeats, ESTs
Anopheles gambiae S AgamS1 ABKQ00000000 Repeats, ESTs
Rhodnius prolixus CDC RproC1 ACPB00000000 Repeats, ESTs, RNA-seq and protein similarities - GenScan ab initio predictions and EST-build genes.

Expression data

There is no new data for this release. However, two small cosmetic changes have been made to the Expression Browser web interface:

  • Where genes are associated with a large number of reporters (a.k.a. probes), we now make more efficient use of screen space so you don't have to scroll so much.
  • Fold-changes are reported in the summaries of "Neighbour t-tests". Previously just the direction (up or down) was reported.

A new search facility is being developed to allow search based on reporters' text expression summaries. Interested users may test the new index at the preview site (example query: permethrin expression). Note: major changes are likely as we improve the utility of this feature. We welcome your feedback on this and any other search-related issues at VectorBase.

Genome browser

There were no upgrades to the genome browser software for this release. Most teething problems associated with the previous release have been fixed, however. We encourage you to report any other issues to the VectorBase helpdesk.

Mitochondrial gene summaries for VectorBase genera

VectorBase's mitochondrial gene sequence resources have been updated using the public nucleotide databases as of January 2011. They are available for the four main genera via the reference species' home pages.

Ontologies

VectorBase supports four ontologies developed by IMBB with members of the research community. These are available for browsing and download.

There are no updates for this release.

Ontology Version Description
MIRO 1.8 An ontology to describe mosquito populations, methods and mechanisms that are used to identify/monitor insecticide resistance.
TGMA 1.1 An ontology to describe the anatomy of mosquitoes.
TADS 1.2 An ontology to describe the anatomy of ticks.
IDOMAL 1.2 An ontology to describe all aspects of malaria. Clinical data, epidemiological data, biological data concerning vertebrate hosts, vectors and parasites as well as interventions and attempts to control the disease.

Tools

As well as adding Rhodnius prolixus data to the BLAST facility at VectorBase, we have made it easier to search the eight Anopheline RNAseq datasets. Simply select "Other organisms" in the main BLAST menu. Results are now linked through to sequence report pages.

Known issues

Please check the VectorBase Twitter page for news on these few remaining issues.

Genome browser: Gene & Transcript pages for GenScan predictions

The Gene and Transcript pages for the GenScan predictions are not activated. This is due to the way the GenScan data are stored in the database. This issue has been addressed and will be sorted for next release.

Please report any problems to the helpdesk.

Release date: 
Monday, February 28, 2011