Release VB_2012-04

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 April release of VectorBase (VB-2012-04) include:

  • Entrez-style search box. Our site search now automatically queries multiple domains and allows one click access to search results across VectorBase data.
  • New gene patches. Aedes, Culex and Ixodes gene sets have all been updated with community-supplied gene improvements.
  • Updated genome browser. VectorBase now runs e! version 66.

Genomes

Patches to the following species to incorporate community gene models:

  • Aedes aegypti (AaegL1.3)
  • Culex quinquefasciatus (CpipJ1.3)
  • Ixodes scapularis (IscaW1.2)

As a result of the gene set patchings, the Compara protein homologies and BioMart have been updated.

Updated Rhodnius prolixus gene build fixing partially overlapping transcripts problem.

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

Search has been upgraded to include an Entrez-style search service. It will automatically search using the provided search term across all domains. These include Genome, Expression Data, Community Annotation, various Ontology, and Population Data domains. Accompanying each domain with results is the number of result hits across that domain for all categories included in it. Simply click on the domain result to be taken to the linked domain hit(s).

Genome browser

Update to Ensembl software and schema version 66.

Mitochondrial gene summaries for VectorBase genera

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/ 2012-02-27
Anopheles Anopheles gambiae http://agambiae.vectorbase.org/SequenceData/Mitochondria/ 2012-02-27
Culex Culex quinquefasciatus http://cquinquefasciatus.vectorbase.org/SequenceData/Mitochondria/ 2012-02-27
Ixodidae and Argasidae Ixodes scapularis http://iscapularis.vectorbase.org/SequenceData/Mitochondria/ 2012-02-27

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 1.1342 An ontology to describe mosquito populations, methods and mechanisms that are used to identify/monitor insecticide resistance.
TGMA 1.10 An ontology to describe the anatomy of mosquitoes.
TADS 1.21 An ontology to describe the anatomy of ticks.
IDOMAL 1.2.3 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.

Ontology browser

TThe Controlled Vocabulary/Ontology browser has been upgraded. Various UI and search enhancements. It is now possible to search for a term by using the numeric portion of the ID.

Known issues

Known issus with this release:

  • Issues with links to external references for the three patches genomes (Ae.aegypti, Cx.quinquefasciatus, Ix.scapularis) - no incorrect data, just missing links to external references, in particular missing gene names and symbol from the community. This will be fixed with the next release.

Please report any problems to the helpdesk.

Release date: 
Monday, April 30, 2012