Release VB_2010-12

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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

The December release of VectorBase (VB_2010-12) contains the first gene set update in over a year (for Anopheles gambiae PEST), and new expression, next-gen transcriptomics and variation data.

Highlights of this release of VectorBase include:

  • New gene set AgamP3.6 for Anopheles gambiae PEST
  • mRNAseq data for eight Anopheline species
  • Wolbachia infection microarray experiment for Aedes aegypti added
  • Genotype data for 60 M, S and Bamako Anopheles gambiae isolates


Genomes

Species Assembly Gene set GenBank WGS
Aedes aegypti Liverpool AaegL1 AaegL1.2 AAGE02000000
Anopheles gambiae PEST AgamP3 AgamP3.6 AAAB01000000
Anopheles gambiae M AgamM1 none ABKP01000000
Anopheles gambiae S AgamS1 none ABKQ01000000
Culex quinquefasciatus JHB CpipJ1 CpipJ1.2 AAWU01000000
Ixodes scapularis Wikel IscaW1 IscaW1.1 ABJB01000000
Pediculus humanus USDA PhumU1 PhumU1.2 AAZO01000000



The AgamP3.6 gene set for Anopheles gambiae is a 'patch' build where manual and community annotations are integrated into the existing set. This process is designed to reflect more accurate annotations for a limited number of loci and not wholescale change of the canonical set. The current gene build includes 65 new genes, 156 new isoform predictions and 443 modified transcript predictions. Follow the link above for a summary of these details, as well as a CDS prediction change log.

Other sequence data

Assembled short-read transcript sequences for eight Anopheline species are now available at VectorBase. You can search by sequence, search by keyword or conserved domain ID, or view alignments graphically in the Anopheles gambiae PEST genome browser (to enable these tracks, click "Configure this page" when in a Location View, then enter "RNAseq" in the search box of the popup window, then choose track display style).
For more details, see this page.

Expression data

One new microarray experiment for Aedes aegypti. Wolbachia infection (Kambris et al, 2009), has been added.
In addition, several new array designs were added to the VectorBase genome browser, including the Affymetrix Anopheles gambiae SNP array and the first for Culex quinquefasciatus (actual expression data will be loaded in a future release). As usual, click "Configure this page" in Location View to enable or disable "probe feature" microarray tracks.
All expression resources for Anopheles gambiae (downloads, BioMart, expression map, expression browser) have been updated to reflect the new gene set.

Genomic variation data

The new release of Vectorbase contains genotypes generated by the AgSNP01 SNPchip on samples of the M/S and Bamako chromosomal forms. Though the chip is a 400k chip, genotypes are provided for 66k of SNPs that were validated by Solexa sequencing and were in Hardy-Weinberg equilibrium, as well as allele frequencies based on these individual calls. Here's an example SNP with genotype data (see the left-hand menu) in the VectorBase genome browser.
Further details about this dataset are contained in Neafsey et al 2010

Ontologies

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

Ontology Version Description
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.
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.


Mitochondrial gene summaries for VectorBase genera

IMBB have collated all mitochondrial gene sequences from the public nucleotide database for the four main genera hosted at VectorBase (Aedes, Anopheles, Culex & Ixodes). These pages are linked from the species homepages e.g. Anopheline mitochondrial genes linked from the Anopheles homepage.

Genome browser

VectorBase uses the Ensembl system to store and present genomic level information about species of interest. This release uses the Ensembl system webcode v60 release, which represents an upgrade from the previous v59. There are no major new features in this release, but please let us know if you have any problems.

A track for the Community Annotation Pipeline has been made accessible as a beta release. We are actively working with EBI to resolve some compatibility issues. It has not yet been added as a default "external" source in the browser, but it may be attached through the "Manager your data" link. General instructions to do this may be found here. However, note that there are currently problems attaching DAS tracks. Sorry for any inconvenience.

Website

VectorBase has expanded the ways in which you can interact with us and get information from the developers and the vector community at large. The Communications panel at the right hand side of the homepage contains a number of RSS feeds, a web form to contact us (if you don't have access to your email) and links to VectorBase's Facebook and Twitter online presences.

Release date: 
Thursday, August 12, 2010