Release VB-2013-08

Overview

We are pleased to announce the August release of VectorBase (VB-2013-08):

  • We invite you all to visit our recently re-launched VectorBase Forum. You can read our forum topics or login to post a question, suggestion comment or reply. Our more recent post include a job opening and a VectorBase workshop announcement.
  • Two new tutorials have been added featuring the use of the Population Biology Browser, Search, the Genome Browser, and the Ontology Browser to visualize and explore single nucleotide polymorphisms (SNP) data. This topic is called "variation data" in VectorBase.
  • Similarity search and downloads now contain data from Musca domestica and Anopheles nili.
  • Genome annotation sets for all species available in GTF format.

Genomes

Released genomes, with gene predictions

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

Genome annotation

No new data for this release.

Population Biology

The following new datasets have been added:

Several "meta-projects" have been added to show data from multiple projects in the same context. Currently these have to be limited to a few thousand samples to keep page-load times reasonable.
Linkage to and from the genome browser variation (SNP) pages has been improved. Some minor cosmetic improvements have been made to the population project, sample and assay browser.

Variation Data

Visualisation of the 2La, 2Rb, 2Rc, 2Rj and 2Ru structural inversions have now been added to the anopheles gambiae variation database.

Expression Data

For this release the expression microarray probes for Anopheles gambiae, Aedes aegypti and Culex quinquefasciatus have been remapped using a new informatics pipeline. Quality control checks for this remapping has indicated that >95% of the probe:gene assignments have remained the same, and that many probes that previously mapped to multiple positions in the genome have been removed. We believe the latest remapping provides a 'cleaner' dataset than previous remappings, but if researchers note any significant changes genes for genes of interest that they believe are incorrect we request they contact us with details of the changes so that we can investigate further.

Please also note that the expression resources have now been updated to the new Aedes aegypti AaegL1.4 gene set. This was a known omission from the previous release.

No new expression experiments have been added for this release.

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 Aedine mitochondrial genes 2013-07-26
Anopheles Anopheles gambiae Anopheline mitochondrial genes 2013-07-26
Culex Culex quinquefasciatus Culicine mitochondrial genes 2013-07-26
Ixodidae and Argasidae Ixodes scapularis Ixodida mitochondrial genes 2013-07-26

Ontologies

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

Ontology Version Description
GAZ 1.512 A controlled vocabulary of geographic locations.
GO 2013-07-25 The gene ontology.
IDODEN 0.7 Beta release of an an ontology that describes all aspects of Dengue. Clinical data, epidemiological data, biological data concerning vertebrate hosts, vectors and viruses as well as interventions and attempts to control the disease.
IDOMAL 1.3 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. This version includes a section describing natural therapies and remedies.
MIRO 2.1 An ontology to describe mosquito populations, methods and mechanisms that are used to identify/monitor insecticide resistance.
TADS 1.22 An ontology to describe the anatomy of ticks.
TGMA 1.12 An ontology to describe the anatomy of mosquitoes. This version contains all the images from the book "Anatomical drawings of the biting flies".

Tutorials

Please take a look of our new tutorials and if you have any questions or comments, please contact us at info@vectorbase.org

Biomarts

The variation biomart in the previous release was discovered to have a bug that prevented retrieval of approximately ~170K SNP entries is the recently added anopheles gambiae MR4 colony dataset. This has been corrected in this release.

Known issues

  • BioMart is in the process of being updated.

Please report any problems to the helpdesk.

Release date: 
Tuesday, August 13, 2013