Release VB_2012-02

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

Please note that we did not make the release scheduled for December 2011. This was due to stability issues with the new hardware which is now hosting the VectorBase website. There will be an additional release in March 2012 to accommodate some genome annotation updates. The regular two-monthly release cycle will continue from May 2012.

Highlights of the February release of VectorBase (VB-2012-02) include:

  • Improved front-page search: genomes, ontologies, expression data and population data are now searchable.
  • Simplified, enhanced new graphical interface to our expression maps.

Genomes

No new genomic data has been released or updated.

Fully released genomes, with gene predictions

Species Assembly Gene set GenBank WGS
Aedes aegypti Liverpool AaegL1 AaegL1.3 AAGE02000000
Anopheles gambiae PEST AgamP3 AgamP3.7 AAAB01000000
Culex quinquefasciatus JHB CpipJ1 CpipJ1.3 AAWU01000000
Ixodes scapularis Wikel IscaW1 IscaW1.2 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.
Glossina morsitansYale GmorY1 - Repeats, RNA-seq (via BAM files) - EST-build genes, SNAP ab initio predictions, MAKER gene predictions.

Search

Searching VectorBase has just become easier. The default search of the genomic data is still there but you can now search the expression data, population biology, community annotations and ontologies from the same search box. Currently you will need to choose which domain to query by using the Domain drop-down menu. In future releases we plan to provide the results from all domains in a more Entrez-like page so that you can see where the search term is found in all parts of the VectorBase site in one, simple step.

Expression data

No new experiments have been added for this release. However, the Anopheles gambiae expression map has been updated to remove an experiment with only two biological replicates that was adversely affecting the clustering.

Expression maps

A simplified and more compact graphical interface for the expression map has been developed. One can now visualize up to three different gene sets/searches (based on gene IDs, gene symbols, InterPro or GO annotations) and also highlight up to three expression characteristics. It is now easier to find the expression maps, either visit the main Expression Data page or use the new text links on any Anopheles gambiae or Aedes aegypti gene expression report page.

Please cite the following paper: http://www.biomedcentral.com/1471-2164/12/620/abstract if you find the expression map useful in your work.

Genome browser

It is now easier to associate PubMed references with VectorBase genes via the genome browser. On any gene page, select the PubMed link in the left-hand menu, then click on the "Add citations" link.

Mitochondrial gene summaries for VectorBase genera

Mitochondrial sequences for genus Anopheles, genus Aedes, family Ixodidae, family Argasidase, genus Culex from GenBank (as of 2011-09-16) have been BLASTed against the corresponding reference mitochondrial genome, and the results have been grouped by matching genes.

Links to Mitochondrial data for the 4 main genera are presented below for convenience.

Genus/genera Reference species Mitochondrial gene resource Last updated
Aedes Aedes aegypti http://aaegypti.vectorbase.org/SequenceData/Mitochondria/ 2011-09-16
Anopheles Anopheles gambiae http://agambiae.vectorbase.org/SequenceData/Mitochondria/ 2011-09-16
Culex Culex quinquefasciatus http://cquinquefasciatus.vectorbase.org/SequenceData/Mitochondria/ 2011-09-16
Ixodidae and Argasidae Ixodes scapularis http://iscapularis.vectorbase.org/SequenceData/Mitochondria/ 2011-09-16

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.

Known issues

Other issues resolved with this release:

  • Addressed a GFF upload problem reported by a VectorBase user. GFFs should be supported by the Ensembl genome browsers this release
  • Added GDAV and a community gene comment page to VectorBase tools
  • Streamlined PubMed ID submission, which are now available directly from the Genome Browser
  • Updated the Rhodnius prolixus genome scaffolds with “soft” masked versions for the VectorBase community

Please report any problems to the helpdesk.

Release date: 
Tuesday, February 28, 2012