Release VB-2013-04

Overview

We are pleased to announce the April release of VectorBase (VB-2013-04). Highlights of this release include:

  • Release genesets for Glossina morsitans and Rhodnius prolixus.
  • Pre-sites including MAKER based gene predictions for Lutzomyia longipalpis, Phlebotomus papatasi & Biomphalaria glabrata.
  • For some queries BLAST is working slowly, we are aware of the issue and are working on a way to fix it. In the mean time please submit only one query (sequence) at the time.
  • Nine Anopheline genome assemblies added for BLAST searching and download from the Anopheles Genomes Cluster.
  • Pathway information from the KEGG database added for mosquitoes (Anopheles gambiae, Aedes aegypti and Culex quinquefasciatus), tick (Ixodes scapularis) and lice (Pediculus humanus) species. Try this sample entry for A. gambiae: AGAP004786.
  • Two new microarray expression experiments have been curated.
  • An improved and searchable Glossary (in the 'General' search category).
  • Do not forget to visit our tutorials page, nine tutorials have been updated and improved for this release including one for BLAST.

Genomes

Released genomes, with gene predictions

Species Assembly Gene set GenBank WGS
Aedes aegypti Liverpool AaegL1 AaegL1.3 AAGE02000000
Anopheles darlingi Coari AdarC1 AdarC1.0 ADMH00000000
Anopheles gambiae PEST AgamP3 AgamP3.7 AAAB01000000
Culex quinquefasciatus JHB CpipJ1 CpipJ1.3 AAWU01000000
Ixodes scapularis Wikel IscaW1 IscaW1.2 ABJB01000000
Pediculus humanus USDA PhumU1 PhumU1.2 AAZO01000000
Rhodnius prolixus CDC RproC1 RproC1.1 ACPB00000000
Glossina morsitans Yale GmorY1 GmorY1.1  
Pre-released genomes, with mapped data and gene predictions
Anopheles stephensi Indian Wild Type AsteI1 AsteI1.0  
Lutzomyia longipalpis Jacobina LlonJ1 LlonJ1.0  
Phlebotomus papatasi Israel PpapI1 PpapI1.0  
Biomphalaria glabrata BB02 BglaB1 BglaB1.0  

Pre-released genomes, with mapped data but no gene predictions

Species Assembly GenBank WGS Project Data available
Anopheles gambiae M AgamM1 ABKP00000000 Repeats, ESTs
Anopheles gambiae S AgamS1 ABKQ00000000 Repeats, ESTs

Variation Data

No new data for this release.

Expression Data

Two new experiments have been added to the Expression Browser, Maps, BioMart and flat file downloads:

Several experiments were wrongly cited (to Marinotti et al., 2005) these have been corrected (Marinotti et al., 2006).

The naming of two arrays (OXFORD Aedes aegypti AGILENT 44k v1 and OXFORD Anopheles gambiae Agilent 44k v1) have been standardised to correct some case inconsistencies.

In addition, a small cosmetic change has been made to gene expression summary pages to provide cleaner links to the genome browser and expression maps.

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 2013-03-19
Anopheles Anopheles gambiae Anopheline mitochondrial genes 2013-03-19
Culex Culex quinquefasciatus Culicine mitochondrial genes 2013-03-19
Ixodidae and Argasidae Ixodes scapularis Ixodida mitochondrial genes 2013-03-19

Ontologies

Release highlight: Added Aedes images to the mosquito anatomy ontology

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 2013-04-02 The gene ontology.
IDODEN 0.3 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 1.2.6 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 2.0 An ontology to describe mosquito populations, methods and mechanisms that are used to identify/monitor insecticide resistance.
TADS 1.21 An ontology to describe the anatomy of ticks.
TGMA 1.11 An ontology to describe the anatomy of mosquitoes.

Tutorials

Follow these links to take a look of the tutorials and for any question, suggestion or comment about them please contact us at info@vectorbase.org.

Known issues

  • BioMart will be updated later in the week. Updated on Thursday 9 May 2013

Please report any problems to the helpdesk.

Release date: 
Tuesday, April 30, 2013