Release VB-2016-10

We are pleased to announce the October 2016 release of VectorBase (VB-2016-10):

  • In this release there have been updates to genes sets for multiple Anopheline species. The latest gene set updates have been derived from community supplied gene annotations for Anopheles arabiensis, Anopheles albimanus, Anopheles funestus, Anopheles gambiae, Anopheles melas, Anopheles merus and Anopheles quadriannulatus.
  • Variation database samples have now been renamed after their PopBio identifiers allowing navigation between the PopBio application and the variation browser via the sample picker application
  • Gene description projections have been performed one-to-many orthologs from
    • Ae. aegypti to Ae. albopictus
    • An. gambiae to the other Anophelines
    • G. morsitans to all other Glossina species, as well as Musca domestcia and Stomoxys calcitrans
    • D. melanogaster to all Glossina species, Musca domestica and Stomoxys calcitrans
  • Two microarray and two RNA-seq experiments have been added to the expression browser for Ixodes scapularis, Aedes aegypti and Anopheles gambiae.
  • Six insecticide resistance studies have been added to the population biology resource.
  • Enabled Galaxy's Trackster visualization
  • VectorBase search now provides downloads of sequences based on search results
  • Improved the VectorBase Search Facet interface
  • Improvements to Search Autocomplete suggestions and performance
  • Three tutorials have been created for this release, the topics covered are: the use of the Expression Browser for microarrays and RNAseq, the use of RNAseq pipelines/workflows with Galaxy and the Sample picker to explore samples metadata

Genomes

Released genomes, with gene predictions

Organism Strain Assembly Gene set Gene Count Browser
Aedes aegypti Liverpool AaegL3 AaegL3.3 17 478
Aedes albopictus Foshan AaloF1 AaloF1.1 17 592
Anopheles albimanus STECLA AalbS1 AalbS1.4 12 534
Anopheles arabiensis Dongola AaraD1 AaraD1.4 13 908
Anopheles atroparvus EBRO AatrE1 AatrE1.3 14 244
Anopheles christyi ACHKN1017 AchrA1 AchrA1.3 11 162
Anopheles coluzzii Mali-NIH AcolM1 AcolM1.3 14 560
Anopheles culicifacies A A-37 AculA1 AculA1.3 14 889
Anopheles darlingi Coari AdarC3 AdarC3.3 10 961
Anopheles dirus WRAIR2 AdirW1 AdirW1.3 13 299
Anopheles epiroticus Epiroticus2 AepiE1 AepiE1.3 12 705
Anopheles farauti FAR1 AfarF2 AfarF2.1 13 462
Anopheles funestus FUMOZ AfunF1 AfunF1.4 13 919
Anopheles gambiae PEST AgamP4 AgamP4.4 13 807
Anopheles maculatus B maculatus3 AmacM1 AmacM1.3 15 050
Anopheles melas CM1001059_A AmelC2 AmelC2.2 15 813
Anopheles merus MAF AmerM2 AmerM2.2 13 718
Anopheles minimus MINIMUS1 AminM1 AminM1.3 13 231
Anopheles quadriannulatus A SANGWE AquaS1 AquaS1.4 14 011
Anopheles sinensis China AsinC2 AsinC2.1 19 815
Anopheles sinensis SINENSIS AsinS2 AsinS2.1 13 331
Anopheles stephensi Indian AsteI2 AsteI2.2 12 350
Anopheles stephensi SDA-500 AsteS1 AsteS1.3 13 764
Biomphalaria glabrata BB02 BglaB1 BglaB1.4 14 420
Cimex lectularius Harlan ClecH1 ClecH1.2 14 085
Culex quinquefasciatus Johannesburg CpipJ2 CpipJ2.2 19 363
Glossina austeni TTRI GausT1 GausT1.3 20 309
Glossina brevipalpis IAEA GbreI1 GbreI1.3 15 032
Glossina fuscipes IAEA GfusI1 GfusI1.3 20 737
Glossina morsitans Yale GmorY1 GmorY1.5 13 034
Glossina pallidipes IAEA GpalI1 GpalI1.3 19 852
Glossina palpalis IAEA GpapI1 GpapI1.1 20 726
Ixodes scapularis Wikel IscaW1 IscaW1.4 20 771
Lutzomyia longipalpis Jacobina LlonJ1 LlonJ1.2 10 494
Musca domestica Aabys MdomA1 MdomA1.2 16 087
Pediculus humanus USDA PhumU2 PhumU2.1 11 699
Phlebotomus papatasi Israel PpapI1 PpapI1.2 12 685
Rhodnius prolixus CDC RproC3 RproC3.1 16 843
Sarcoptes scabiei var. canis Arlian SscaA1 SscaA1.1 10 679
Stomoxys calcitrans USDA ScalU1 ScalU1.1 16 636

Expression data

The four new differential expression experiments are:

See known issues section below.

Population Biology/Insecticide Resistance

Data from six insecticide resistance papers have been added:

See known issues section below.

Variation Data

Summary of available variation data by organism

    Reference species SNP calls (million) Indel calls (million) Last dataset update Last variation effect update
    Aedes aegypti 0.33 0.004 2016-02 2016-02
    Anopheles arabiensis 10.2 0.98 2014-10 2016-10
    Anopheles culicifacies 9.15 0.88 2014-10 2015-10
    Anopheles epiroticus 3.28 0.25 2014-10 2015-08
    Anopheles farauti 6.5 0.75 2015-06 2015-06
    Anopheles funestus 12.9 0.47 2014-10 2016-10
    Anopheles gambiae 7.3 1.3 2016-02 2016-10
    Anopheles melas 3.7 0.41 2015-06 2016-10
    Anopheles merus 6.1 0.53 2015-06 2016-10
    Anopheles minimus 4.21 0.22 2014-10 2015-08
    Anopheles quadriannulatus 10.1 0.89 2014-10 2016-10
    Anopheles sinensis 5.84 0.41 2015-06 2015-06
    Anopheles stephensi SDA-500 5.8 0.57 2014-10 2015-08
    Anopheles stephensi Indian 0.37 2014-10 2015-06
    Ixodes scapularis 1.78 2015-02 2015-06

    Tutorials

    Follow this link for all the site tutorials, which includes material such as videos with its slides, practice exercises with answer keys, and sample files. Visit our new YouTube and youku Channels to watch all our video tutorials, we plan to add one for each release. The video slides (including demo outlines), are in our regular tutorial pages. The new tutorials for this release are:

    • Sample search and Sample picker
    • Transcript data and resources for microarrays and RNAseq
    • VectorBase Galaxy

    Known issues

    Please report any problems to the helpdesk.


    Future releases

    The next VectorBase release (VB-2016-12) is scheduled for mid December.

    Release date: 
    Thursday, October 20, 2016