Release VB-2014-04


We are pleased to announce the April release of VectorBase (VB-2014-04):

  • Genome assembly updates for Anopheles gambiae, Anopheles darlingi, Aedes aegypti, Culex quinquefasciatus & Pediculus humanus
  • Geneset updates for An. gambiae, An. darlingi, Ae. aegypti, Cx. quinquefasciatus & P. humanus
  • NIAID Arthropod vector-derived cell line transcriptomes for 4 species included. This is the first RNAseq for Ixodes
  • BLAST, ClustalW, HMMer compute cores moved to new hardware. This conversion cleared out all past job results.
  • VectorBase servers were patched for the Heartbleed Vulnerability within 24 hours of public disclosure and are no longer vulnerable. The server certificates were also reissued and the old certificates revoked shortly after. Although the chances of data compromise is minimal, it is recommended that users change their passwords in case of a compromise of login credentials.
  • In order to make it easier to find help and documentation about VectorBase data, tools and resources, the tutorials page just got an overhaul. Please follow this link to take a look at it.
  • Seven new tutorials about manual annotation have been created for this release, these are a detailed step by step guide of the process using Artemis. Our overview tutorial about VectorBase tools has been updated.
  • Follow these links to watch four new video tutorials covering topics such as a VectorBase Tour and different aspects of the Population Biology Browser (PopBio), highlighting its relationship with Advanced Search and the Genome Browser.


VectorBase is committed to a new release every two months with all data freely available for public use based on NIH/NIAID policy.

For your species of interest, click on Organism, Strain, Assembly, or Gene set to find the Genome Browser link (which looks like this:  ).

Pre-released genomes, with mapped data and gene predictions

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

Species Assembly GenBank WGS Data available
Anopheles gambiae S AgamS1 ABKQ00000000 Repeats, ESTs

Genome assembly

Five species have updated assemblies for this release:

  • Inclusion of mitochondrial genomes for Ae. aegypti, An. gambiae, Cx. quinquefasciatus & P. humanus
  • Synchronisation of An. darlingi with the submitted assembly at NCBI. This adds 60 small scaffolds.

Genome annotation

  • An. gambiae update includes loci predicted via 1:1 orthology across the 16 Anopheline genomes and the mitochondrially encoded genes.
  • Ae. aegypti, Cx. quinquefasciatus & P. humanus include the mitochondrially encoded genes.
  • An. darlingi update includes ncRNAs predicted on the new scaffolds, no change to the protein-coding component.

Transcriptomics (RNAseq)

  • RNAseq for four additional Anopheline species included: An. atroparvus, An. farauti, An. merus & An. sinensis
  • NIAID Arthropod Vector-derived Cell line transcriptomes from 4 species (Ae. aegypti, An. gambiae, An. stephensi & Ix. scapularis) with replicates

Expression Data

No new data, but all expression resources have been rebuilt to incorporate minor updates to the AgamP4.1 and AaegL3.1 gene sets.

Population Biology/Insecticide Resistance

Added six new insecticide resistance studies:

Malaria Atlas Project

The mosquito observation data used to create the Mosquito Maps at the Malaria Atlas Project have been imported into VectorBase as four separate population biology projects:

In addition, we have significantly improved page load times on big projects with maps and/or graphs, and have improved the display of population biology search results with more useful descriptions where available. Date-range search is now available in Advanced Search.

Variation Data

Anopheles gambiae variation effect consequences updated to accomodate changes made to gene models in this release

Added new variation data track that identifies the SNP loci implicated in resistance to Serratia marcescens infection in An. gambiae as detailed in the recent publication 'Genetic Dissection of Anopheles gambiae Gut Epithelial Responses to Serratia marcescens',Stathopoulous et al, PLoS Pathogens (2014).

New feature
Sample picker display.

In this release we have produced a trial interface for selecting samples for display on the variation transcript comparison image display*. This display shows the DNA variations present in different samples in their context on a given transcript. The large number of samples in the variation databases for some species (e.g. anopheles gambiae) makes selecting samples for display very difficult both because the list of samples is very long, and because useful descriptions of the samples are missing. We have attempted to address these issues by providing two different sample selection pathways via the "configure this page" option,

  1. Selected individuals.
    The original selection method has been upgraded to display sortable cloumns of sample names and brief sample descriptions. If you know which samples you wish to display then this display should let you rapidly find and select the samples you are interested in.
  2. Individual metadata.
    This is a new selection method that shows sample metadata derived from a selection of BioSample database records. This display indicates for a given metadata term (such as karyotype patterns, insecticide resistance data, or sampling locations) how many samples share this term, and allows all of the samples to be simultaneously selected for visualization in the transcript comparison image display. This display is best suited to exploring the samples present in the database and discovering new samples of interest.

There are a number of things to note about the new "individual metadata" selection procedure.

  1. For the new "individual metadata" selection method we have initially limited which sample metadata terms can be selected to those where Some metadata terms may appear that do not seem to make much sense (e.g. you may see terms for a species other than those you were expecting to see). This is becuase we derive the metadata terms from external databases and cannot control the content of those records, so if a study cites both anophles gambiae and anopheles arabiensis
    then both species terms will appear in the metadata display.
  2. These alterations are not confirmed features for future Vectorbase releases - they are currently on trial and we would like feedback from the community about these modifications. We are interested in improving the linkage of sample information to variation data so that more effective displays can be produced for our users, so we are particularly interested in hearing of examples of how you would like to be able to interrogate and visualize the data.

* To use this facility go to any transcript display tab in the genome browser and select the comparison image option in the left hand menu. Then choose "configure this page" from the left hand menu, and try working with the "selected individuals" and "individual metadata" options.

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 2014-04
Anopheles Anopheles gambiae Anopheline mitochondrial genes 2014-04
Culex Culex quinquefasciatus Culicine mitochondrial genes 2014-04
Ixodidae and Argasidae Ixodes scapularis Ixodida mitochondrial genes 2014-04


Ontology Version Description Changes in this release
GAZ 1.512 A controlled vocabulary of geographic locations.
GO 2014-02-12 The gene ontology. Updated to 2014-04-14 daily release.
IDODEN 0.18 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. Added terms for neutralization assays.
IDOMAL 1.36 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. Additions and changes of Anopheline species names.
MIRO 2.2 An ontology to describe mosquito populations, methods and mechanisms that are used to identify/monitor insecticide resistance. Additions and changes of Anopheline species names.
TADS 1.22 An ontology to describe the anatomy of ticks.
TGMA 1.12 An ontology to describe the anatomy of mosquitoes.


Follow this link for to the new tutorials page, the updated and newly created VectorBase tutorials and videos.

Known issues

  • A very small minority (<1%) of Malaria Atlas Project field collection records in the population biology resource contain corrupted date information (dates appear to be negative). This will be fixed in the next release.

Please report any problems to the helpdesk.

Release date: 
Wednesday, April 30, 2014