Release VB_2010-10

lawson's picture
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 October release of VectorBase (VB_2010-10) contains an update to the genome browser component, a preliminary Anopheles gambiae M & S genome browser, as well as an update of various data sets.

Highlights of this release of VectorBase include:

  • Updated genome browser to Ensembl e!59 release.
  • Updated search indices.
  • Anopheles gambiae M and S genome browsers with EST mapping, EST-based genes and repeats. Note that the EST-based genes ARE NOT the final gene set, they are only provided as support for the community. There is no plan to maintain the identifiers or even the gene structure.
  • Update Xrefs for Anopheles gambiae, Aedes aegypti and Culex quinquefasciatus.
  • Updated genome browser to Ensembl e!58 release.

Other improvements include the standard changes for a new release (search re-indexing to capture new data, updated BioMarts for all species, comparative analysis for all species providing ortholog/paralog predictions)

Genomes

Species Assembly Gene set GenBank WGS
Aedes aegypti Liverpool AaegL1 AaegL1.2 AAGE02000000
Anopheles gambiae PEST AgamP3 AgamP3.5 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


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 v59 release.
Highlights of this release include:

  • Anopheles gambiae M and S preliminary genome browsers. Repeats and EST were mapped to the genomes. EST-based genes were build as a support for the community but not that those are not the final gene set. There is no plan to maintain the identifiers or even the gene structure.
  • The Anopheles gambiae DAS track Mass spec. proteomics (JHU II): used to have problems displaying large numbers of peptide features. This has now been solved.
  • Multiple identical features are now grouped together. To turn on/off DAS and other tracks, click on "Configure this page" while in any "Location view".

Please note that the "Configure this page" window now has a tick icon in the top right hand corner instead of the "save and close" text displayed in the previous version of the genome browser.

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.


Genomic variation data

The genome browser now shows the locations and consequences (e.g. synonymous, non-synonymous) of SNPs present on the forthcoming Affymetrix Anopheles gambiae SNP-chip. Genotypes for approximately 60 field isolates will be added in the December release.

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.

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: 
Wednesday, February 10, 2010