Release VB-2017-04

We are pleased to announce the April 2017 release of VectorBase (VB-2017-04):

  • The Aedes albopictus C6/36 cell line assembly (canu_80X_arrow2.2) data are available from the Downloads section
  • In this release there have been updates to genes sets for twelve Anopheline species. The latest gene set updates have been derived from community supplied gene annotations for Anopheles arabiensis, Anopheles albimanus, Anopheles darlingi, Anopheles dirus, Anopheles farauti, Anopheles funestus, Anopheles gambiae, Anopheles melas, Anopheles merus, Anopheles minimus, Anopheles quadriannulatus and Anopheles stephensi.
  • Microarray probe mappings and variation consequence effects have been updated for all species.
  • New ortholog metrics have been added to help with the identification of "high confidence" orthologs. A new FAQ discusses the new metrics, such as the Gene Order Conservation (GOC) score.
  • Four new differential expression experiments added.
  • Fourteen new population biology datasets added, including sample metadata from the MalariaGen 1000 Anopheles gambiae genomes project, insecticide resistance studies and several large new blood meal species identification studies.
  • BLAST has been been updated to allow sorting across all organism hits, by utilizing the expand all and sort all buttons.
  • New options for higher e-values were added to BLAST. Previously, our highest e-value allowed was 10. Current options include 100, 1000, 10000 and 100000. You can test this new feature when using protein queries against scaffolds in tBLASTn for the search of (new) highly derived/rapidly evolving genes.
  • Three tutorials have been updated for this release: BioMart, BLAST and Web Apollo.
  • New page for workshops, meetings, and conferences attended by VectorBase.
  • Search page now allows users to search using a file

Genomes

Released genomes, with gene predictions

Organism Strain Assembly Gene set Gene Count Browser
Aedes aegypti Liverpool AaegL3 AaegL3.4 16 955
Aedes albopictus Foshan AaloF1 AaloF1.2 18 294
Anopheles albimanus STECLA AalbS2 AalbS2.3 12 500
Anopheles arabiensis Dongola AaraD1 AaraD1.6 13 830
Anopheles atroparvus EBRO AatrE1 AatrE1.4 14 113
Anopheles christyi ACHKN1017 AchrA1 AchrA1.4 11 081
Anopheles coluzzii Mali-NIH AcolM1 AcolM1.4 14 891
Anopheles culicifacies A A-37 AculA1 AculA1.4 14 713
Anopheles darlingi Coari AdarC3 AdarC3.5 10 958
Anopheles dirus WRAIR2 AdirW1 AdirW1.5 13 216
Anopheles epiroticus Epiroticus2 AepiE1 AepiE1.4 12 547
Anopheles farauti FAR1 AfarF2 AfarF2.3 13 325
Anopheles funestus FUMOZ AfunF1 AfunF1.6 13 920
Anopheles gambiae PEST AgamP4 AgamP4.6 13 756
Anopheles maculatus maculatus3 AmacM1 AmacM1.4 15 016
Anopheles melas CM1001059_A AmelC2 AmelC2.4 15 726
Anopheles merus MAF AmerM2 AmerM2.4 13 664
Anopheles minimus MINIMUS1 AminM1 AminM1.5 13 078
Anopheles quadriannulatus SANGWE AquaS1 AquaS1.6 13 959
Anopheles sinensis China AsinC2 AsinC2.2 19 694
Anopheles sinensis SINENSIS AsinS2 AsinS2.2 13 170
Anopheles stephensi Indian AsteI2 AsteI2.3 12 189
Anopheles stephensi SDA-500 AsteS1 AsteS1.5 13 601
Biomphalaria glabrata BB02 BglaB1 BglaB1.5 15 912
Cimex lectularius Harlan ClecH1 ClecH1.3 15 292
Culex quinquefasciatus Johannesburg CpipJ2 CpipJ2.3 19 796
Glossina austeni TTRI GausT1 GausT1.4 20 117
Glossina brevipalpis IAEA GbreI1 GbreI1.4 14 972
Glossina fuscipes IAEA GfusI1 GfusI1.4 20 514
Glossina morsitans Yale GmorY1 GmorY1.6 12 809
Glossina pallidipes IAEA GpalI1 GpalI1.4 19 650
Glossina palpalis IAEA GpapI1 GpapI1.2 20 526
Ixodes scapularis Wikel IscaW1 IscaW1.5 23 340
Lutzomyia longipalpis Jacobina LlonJ1 LlonJ1.3 10 513
Musca domestica Aabys MdomA1 MdomA1.3 16 135
Pediculus humanus USDA PhumU2 PhumU2.2 11 713
Phlebotomus papatasi Israel PpapI1 PpapI1.3 11 615
Rhodnius prolixus CDC RproC3 RproC3.2 15 741
Sarcoptes scabiei var. canis Arlian SscaA1 SscaA1.2 10 797
Stomoxys calcitrans USDA ScalU1 ScalU1.2 16 874

Expression data

New experiments processed and added to the expression browser:

Population Biology/Insecticide Resistance

14 projects have been added:

8 projects have been updated (usually to fix minor data inconsistencies):

In this release, the population biology project pages have been updated. The old Google Maps, bar charts and dot plots have been removed, and replaced with a link to the PopBio Map. In future releases we aim to improve the charting functionality of the PopBio Map, which currently produces basic plots in insecticide resistance view.

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 2017-04
    Anopheles arabiensis 10.2 0.98 2014-10 2017-04
    Anopheles culicifacies 9.15 0.88 2014-10 2017-04
    Anopheles epiroticus 3.28 0.25 2014-10 2017-04
    Anopheles farauti 6.5 0.75 2015-06 2017-04
    Anopheles funestus 12.9 0.47 2014-10 2017-04
    Anopheles gambiae 7.3 1.3 2016-02 2017-04
    Anopheles melas 3.7 0.41 2015-06 2017-04
    Anopheles merus 6.1 0.53 2015-06 2017-04
    Anopheles minimus 4.21 0.22 2014-10 2017-04
    Anopheles quadriannulatus 10.1 0.89 2014-10 2017-04
    Anopheles sinensis 5.84 0.41 2015-06 2017-04
    Anopheles stephensi SDA-500 5.8 0.57 2014-10 2017-04
    Anopheles stephensi Indian 0.37 2014-10 2017-04
    Ixodes scapularis 1.78 2015-02 2017-04

    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:

    • BioMart
    • BLAST
    • Web Apollo


    Known issues

    • The project contact Matthew B. Thomas (Center for Infectious Disease Dynamics and Department of Entomology, Pennsylvania State University, University Park, PA, 16802, USA) has been omitted from PopBio project VBP0000162. This will be rectified as soon as possible.

    Future releases

    The next VectorBase release (VB-2017-06) is scheduled for late June.

    Please report any problems to the helpdesk.

    Release date: 
    Tuesday, April 25, 2017