Release VB-2013-10

Overview

We are pleased to announce the October release of VectorBase (VB-2013-10):

  • Updated genome assembly and annotations for Anopheles stephensi Indian Wild type strain (Jake Tu, Virginia Tech)
  • Release of the remaining 7 Anopheles genome assemblies from the Anopheles Genome Cluster
  • Nine Anopheles genome annotations included in compara and biomart.
  • Inclusion of 5 expression studies for Aedes aegypti
  • Multiple interface improvements to BLAST, HMMer and ClustalW tools including an improved uniform progress box and the option to upload files
  • HMMmer and ClustalW job parameters for saved jobs automatically can be reused for logged in users
  • A minor update/fix to the Glossina annotation impacting ten genes: 4 new additions and a split into 5 separate transcripts
  • Improved readability and information content of download URLs for VectorBase data

Genomes

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

Release of the Anopheles stephensi genome assembly and annotations
The An. stephensi Indian Wild type strain has an improved genome assembly and a complete re-annotation via MAKER (performed by the Virginia Tech). This is currently integrated into VectorBase as a pre-site (i.e. not included in the comparative analyses and BioMart tools) but this is scheduled for the December release. RNAseq evidence is available via the track configuration in the region in detail displays.

Expression Data

Several experiments/publications have been added for Aedes aegypti:

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 2013-10
Anopheles Anopheles gambiae Anopheline mitochondrial genes 2013-10
Culex Culex quinquefasciatus Culicine mitochondrial genes 2013-10
Ixodidae and Argasidae Ixodes scapularis Ixodida mitochondrial genes 2013-10

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".

Known issues

  • Some blast datasets are missing (Anopheles stephensi Indian peptides). These will be copied as soon as possible.

Please report any problems to the helpdesk.

Release date: 
Tuesday, October 8, 2013