Release VB_2010-08

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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 August release of VectorBase (VB_2010-08) contains an update to the genome browser component, updated alignment of cDNA/ESTs as well as updates to ontologies and new expression microarray data sets.

Highlights of this release of VectorBase include:

  • Updated genome browser to Ensembl e!58 release.
  • Three Aedes aegypti expression studies added.
  • Update to the mitochondrial gene data for Aedes, Anopheles, Culex and Ixodes.

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
Culex quinquefasciatus JHB CpipJ1 CpipJ1.2 AAWU01000000
Ixodes scapularis Wikel IscaW1 IscaW1.1 ABJB01000000
Pediculus humanus USDA PhumU1 PhumU1.2 AAZO01000000


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 1.1 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.


Expression studies

Three new expression studies have been integrated into VectorBase (see table) bringing the total number to 35. A full list of experiments is available from the VectorBase Gene expression portal.

Species Citation Description Type
Aedes aegypti Harker ''et al''., 2007 Female vs. Male Microarray
Aedes aegypti Harker ''et al''., 2007 Developmental stages Microarray
Aedes aegypti Harker et al., 2008 Dengue infection, refractory vs. susceptible mosquito strains Microarray


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.

Updated 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 v58 release.

Highlights of this release include:

  • Better navigation between species via a drop-down menu in the header banner
  • More control over tables including which columns to display and making those columns sortable (e.g. AGAP001797).
  • Many bug fixes, for example the gene tree popup menus no longer have the ability to crash your web browser.


Known issues

Genome browser: "500 Internal error"
We have seen this error for gene pages (it may affect others), and it can be solved by removing all cookies for vectorbase.org in your web browser.

Genome browser: DAS tracks "bad hostname" error
We are experiencing problems with the server running the genome browser software. If you enable DAS tracks for Location or Gene views (look for the "Configure this page" link on the left hand side) and see the "bad hostname" error, please contact the VectorBase developers at info@vectorbase.org.

Genome browser: Gene page external data
We regret that the "Community Annotation" DAS source is currently not working properly.

Release date: 
Sunday, August 1, 2010