Release VB_2010-06

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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 June release of VectorBase (VB_2010-06) brings together significant changes to the look and feel of the genome browser component with an update of the Ensembl web code as well as additional data sets in all areas (genomes, ontologies and expression studies).

Highlights of this release of VectorBase include:

  • New genome browser.
  • Addition of a new species Pediculus humanus, the human body louse.
  • IDOMAL malaria ontology.
  • Four Anopheles gambiae expression studies added.
  • Update to the mitochondrial gene data for Anopheles and Ixodes and introduction of similar resources for Aedes and Culex.

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 1.81 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 1.20 An ontology to describe the anatomy of ticks.


Expression studies

Five 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
Anopheles gambiae Félix ''et al''., 2010 Plasmodium berghei infection: midgut Microarray
Anopheles gambiae Félix ''et al''., 2010 Plasmodium berghei infection: fat body Microarray
Anopheles gambiae Pinto et al., 2010 Hemolymph, carcass and head Microarray
Anopheles gambiae Pinto et al., 2010 Hemocyte response to Plasmodium berghei infection Microarray
Aedes aegypti David et al., 2010 Transcriptome response to pollutants and insecticides Next Gen

This Next-gen sequencing-based experiment is only loosely integrated into VectorBase. The data is available for browsing and searching and via the External data left-hand menu on Aedes aegypti gene pages.

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 home pages.

Updated Genome browser

VectorBase uses the Ensembl system to store and present genomic level information about species of interest. Back in November 2008 Ensembl moved to a new website design which offered better methods for user customisation and navigation. Many users will already have seen this if they have used Ensembl or Ensembl Genomes. We have been trialling this webcode for the past couple of months and this release marks the changeover to the Ensembl system webcode v56.

We have updated our Tutorials in light of these changes and there are excellent tutorials from the Ensembl project itself covering aspects of genome browsing. However, if you are still finding it difficult to access data then please contact our info@vectorbase.org helpdesk.

The new genome browser has a different URL style, but we have tried to ensure every old-style link is redirected to the new site. If you have bookmarks or links that are not redirecting properly, please let us know and we will fix it for you.

Known issues

Microarray probe features

There is an issue with the new genome browser where in the genomic location view, if you are zoomed in too far (below about 5kb) the microarray probes disappear from view. Note that you have to enable the microarray tracks by clicking on Configure this page (left menu) → Main panel (main tabs of popup) → Oligo features (left menu of popup) and finally click Save and close (top right corner of popup).

Search index

Some gene symbols and gene, transcript and protein IDs have not yet been added to the VectorBase homepage search index. In the short term we have removed the search facility from the home page but you can perform searches against the full indices using the genome browser search facility.

You may find the search facilities on the following pages more up to date.

  • Anopheles gambiae (AGAP* identifiers)
  • Aedes aegypti (AAEL* identifiers)
  • Ixodes scapularis (ISCW* identifiers)
  • Culex quinquefasciatus (CPIJ* identifiers)
  • Pediculus humanus (PHUM* identifiers)

Personal annotation
The new genome browser allows comments to be attached to gene and transcript pages via the External Data left-hand menu.
This feature is not available in VectorBase at present.

Release date: 
Thursday, January 7, 2010