Release VB-2014-06


We are pleased to announce the June release of VectorBase (VB-2014-06):

  • The house fly (Musca domestica) has been added into VectorBase to facilitate comparative analysis with dipteran vectors.
  • Eighteen more insecticide resistance data from the original IRBase resource are now available in our new Population Biology resource. This will immediately allow new visualizations and will allow building integrated views of genetic, resistance and even pathogen data.
  • Gene set updates for 7 members of Anopheles cluster based on automatic annotation and comparative approaches.
  • Gene ontology (GO) added for Anopheles coluzzi (former M), Biomphalaria glabrata, Lutzomyia longipalpis and Phlebotomus papatasi via Interpro annotations.
  • Variation databases for 6 Anophelines, Aedes aegypti and the tick Ixodes scapularis.
  • We are hosting the annotation software Web Apollo, the manual annotations created here will be collected by VectorBase to update the gene sets, you do not need to submit any files to us. As a transition period, during the next two months we will continue to receive GFF3 files for gene annotations generated with softwares such as Artemis.
  • The Ensembl genome browser has been updated to version 75. New features include the ability to define a region to view/annotate in our new WebApollo instances.
  • Seven of the tutorials and/or their practice exercises have been updated for this release. Additionally, we are also providing a link to Web Apollo user guide.
  • Blast, ClustalW, and Hmmer have job numbers locked to the user that created them. Jobs that are created while not logged in will be accessible to anyone until they are deleted periodically by VectorBase. User jobs that are not saved will also be deleted periodically.


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 assemblies

  • New genome assemblies available for similarity searches include 4 Glossina spp.
    • Glossina austeni
    • Glossina brevipalpis
    • Glossina fuscipes
    • Glossina pallidipes

Genome annotation

  • Musca domestica, the house fly annotations were produced by the NCBI RefSeq group.
  • Updates to correct the starts of gene predictions using MAKER and comparative multiple-sequence alignments were performed for the following 8 Anopheles spp.
    • Anopheles atroparvus, AatrE1.2
    • Anopheles coluzzii, AcolM1.1
    • Anopheles culicifacies, AculA1.2
    • Anopheles farauti, AfarF1.2
    • Anopheles maculatus, AmacM1.2
    • Anopheles melas, AmelC1.2
    • Anopheles merus, AmerM1.2
    • Anopheles sinensis, AsinS1.2

Expression Data

No new data for this release.

Population Biology/Insecticide Resistance

Added 18 new insecticide resistance studies:

Variation Data

New data

New variation databases have been created for the following organisms.

    Reference species SNP calls (million) Indel calls (million) Last updated
    Anopheles arabiensis 10.2 0.98 2014-06
    Anopheles culicifacies 9.15 0.88 2014-06
    Anopheles epiroticus 3.28 0.25 2014-06
    Anopheles funestus 12.9 0.47 2014-06
    Anopheles minimus 4.21 0.22 2014-06
    Anopheles quadriannulatus 10.1 0.89 2014-06
    Ixodes scapularis 1.19 2014-06


    A new set of 220k SNP calls from three insecticide resistant Aedes aegypti Bora-Bora derived strains have been added, as described in the paper

    Comparative analysis of response to selection with three insecticides in the dengue mosquito Aedes aegypti using mRNA sequencing. David JP, Faucon F, Chandor-Proust A, Poupardin R, Riaz MA, Bonin A, Navratil V, Reynaud S.

    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 2014-06
    Anopheles Anopheles gambiae Anopheline mitochondrial genes 2014-06
    Culex Culex quinquefasciatus Culicine mitochondrial genes 2014-06
    Ixodidae and Argasidae Ixodes scapularis Ixodida mitochondrial genes 2014-06


    Ontology Version Description Changes in this release
    GAZ 1.512 A controlled vocabulary of geographic locations.
    GO 2014-06-12 The gene ontology. Updated to the 2014-06-12 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.
    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.
    MIRO 2.2 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.


    Follow this link for the tutorials page, which also includes videos, practice exercises, and sample files.

    Known issues

    • It is not possible to upload files to WebApollo yet, this will get fix in early July.

    Please report any problems to the helpdesk.

    In memory of VectorBase alumni Dr. Martin Hammond

    We dedicate this release of VectorBase to Dr. Martin Hammond, one time outreach officer, VectorBase gene builder and eternally enthusiastic, inquisitive scientist Martin passed away recently after a battle with motor neurone disease. Martin came to EMBL-EBI after many years teaching science at undergraduate level, joining the Ensembl team before becoming instrumental in the Anopheles gambiae project that developed into VectorBase. Post EMBL-EBI he returned to teaching at the University of East Anglia in Norwich. A keen cyclist with a keener mind, he is much missed.

    Release date: 
    Wednesday, June 25, 2014