Release VB-2016-04

We are pleased to announce the April 2016 release of VectorBase (VB-2016-04):

  • New organism Cimex lectularius (Harlan strain)
  • New Aedes aegypti gene expression profiling data for three flavivirus infection time courses (Dengue, West Nile and Yellow Fever viruses)
  • New mass spectrometry data for Anopheles gambiae and Ixodes scapularis
  • Updated InterPro domain annotation of all VectorBase genomes
  • InterPro domain annotation of all transcriptome assemblies
  • New date search in the PopBio map
  • A single nucleotide polymorphism (SNP) calling workflow added to Galaxy
  • New password expiry requirements
  • We have restructured and greatly improved the "About" page. It is design to give current and new users a quick guide of what can be done with the site, including some sample queries with analyses, and much more
  • The "Search" tutorial has been updated, the material includes practice exercises with answer key, and new video with its slides
  • We now have a YouTube Channel were we will add video tutorials. This time we invite you to watch "Tour", which is a (6 min) overview of the site navigation, data types, tools and resources

New password expiry requirements

VectorBase users who have an account will be required to update the password every six months. Thirty (30) days before that an email will be sent to account holders to create a new password, the email will have the necessary links and instructions. You do not need to update your Web Apollo password, this is a separate account.

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 AalbS1.3 12 509
Anopheles arabiensis Dongola AaraD1 AaraD1.3 13 849
Anopheles atroparvus EBRO AatrE1 AatrE1.3 14 244
Anopheles christyi ACHKN1017 AchrA1 AchrA1.3 11 162
Anopheles coluzzii Mali-NIH AcolM1 AcolM1.2 14 711
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 AfunF1.3 13 884
Anopheles gambiae PEST AgamP4 AgamP4.3 13 793
Anopheles maculatus B maculatus3 AmacM1 AmacM1.3 15 050
Anopheles melas CM1001059 AmelC2 AmelC2.1 15 850
Anopheles merus MAF AmerM2 AmerM2.1 13 798
Anopheles minimus MINIMUS1 AminM1 AminM1.3 13 231
Anopheles quadriannulatus A SANGQUA AquaS1 AquaS1.3 13 992
Anopheles sinensis SINENSIS AsinS2 AsinS2.1 13 331
Anopheles sinensis China AsinC2 AsinC2.1 19 815
Anopheles stephensi SDA-500 AsteS1 AsteS1.3 13 764
Anopheles stephensi Indian AsteI2 AsteI2.2 12 350
Biomphalaria glabrata BB02 BglaB1 BglaB1.3 14 423
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 MdomA1.1 15 803
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

In this release we have added the Harlan strain of Cimex lectularius (the bed bug). Protein features for all species have been updated, using InterPro version 55.0.

Expression data

In this release we have added a new experiment profiling gene expression in response to several different flavivirus infections.

Population Biology/Insecticide Resistance

Four insecticide resistance papers have been added:

These are all available in the PopBio map which now has newly added date and normalized insecticide resistance value search functionality.

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 2015-08
    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 2015-06
    Anopheles gambiae 7.3 1.3 2016-02 2016-02
    Anopheles melas 3.7 0.41 2015-06 2015-06
    Anopheles merus 6.1 0.53 2015-06 2015-06
    Anopheles minimus 4.21 0.22 2014-10 2015-08
    Anopheles quadriannulatus 10.1 0.89 2014-10 2015-08
    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

    No variation updates have been performed this release.

    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 Channel 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 and updated tutorials for this release are:


    Future releases

    The next VectorBase release (VB-2016-06) is scheduled for late June.

    Other known issues

    • The tools for the Variation Effect Predictor (VEP) and gene id updates are currently unavailable. We are working to correct this, and will update the release notes as soon as the tools can be used.
    • The PopBio map has a new seasonal search facility. However, please note that this is not yet working to our full satisfaction, and consider this as a "beta" feature. We plan to announce a fully working version in the next release.

    Please report any problems to the helpdesk.

    Release date: 
    Thursday, April 28, 2016