Release VB-2017-02

We are pleased to announce the February 2017 release of VectorBase (VB-2017-02):

  • Updates to all species for RNA gene sets using alignment to Rfam (release 12.1) covariance models, and predictions from miRBase (release 21) and tRNAscan-SE. (Further details)
  • Microarray probe mappings and variant effects have been updated for all species in light of the RNA gene model changes in this release
  • The xref entries for gene symbols are now only attached to genes, and are no longer attached to transcripts
  • New RNAseq track hub data has been added for the following species
    • Aedes aegypti (+4 track hubs)
    • Anopheles gambiae (+3)
    • Anopheles stephensi (+1)
    • Musca domestica (+1)
    • Sarcoptes scabiei (+1, new)
    • Phlebotomus papatasi (SRA version replacement)

    Please note that as stated in the August 2016 (2016-08) VectorBase release notes the old style RNAseq search interface has been retired, and all RNAseq search functionality has now been incorporated into the standard site search facility. RNAseq alignments are now derived from the HISAT pipeline, and the old alignments generated by other methods have been retired.

  • Four new RNA-seq differential expression experiments added to the expression browser
  • Ten new population biology datasets added (and eight updated to improve data consistency)
  • The Web Apollo annotation tool has been upgraded to v2.0.5
  • The Galaxy tool has been upgraded to v16.10
  • Multiple minor updates have been made to the VectorBase search interface.
  • Download limits removed for logged in users. If you want an account, please contact us.
  • New Web Apollo tutorial and PopBio video tutorial
  • New pages with information about VectorBase standard (in-person) and webinar workshops.

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 AalbS2.2 12 431
Anopheles arabiensis Dongola AaraD1 AaraD1.5 13 770
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 AdarC3.4 10 919
Anopheles dirus WRAIR2 AdirW1 AdirW1.4 13 166
Anopheles epiroticus Epiroticus2 AepiE1 AepiE1.4 12 547
Anopheles farauti FAR1 AfarF2 AfarF2.2 13 352
Anopheles funestus FUMOZ AfunF1 AfunF1.5 13 839
Anopheles gambiae PEST AgamP4 AgamP4.5 13 760
Anopheles maculatus B maculatus3 AmacM1 AmacM1.4 15 016
Anopheles melas CM1001059_A AmelC2 AmelC2.3 15 718
Anopheles merus MAF AmerM2 AmerM2.3 13 632
Anopheles minimus MINIMUS1 AminM1 AminM1.4 12 991
Anopheles quadriannulatus A SANGWE AquaS1 AquaS1.5 13 907
Anopheles sinensis China AsinC2 AsinC2.2 19 694
Anopheles sinensis SINENSIS AsinS2 AsinS2.2 13 170
Anopheles stephensi SDA-500 AsteS1 AsteS1.4 13 502
Anopheles stephensi Indian AsteI2 AsteI2.3 12 189
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

Links within the expression browser to experiment pages have now been shortened and simplified. This should make it more convenient to send URLs to colleagues. The experiments listed below are using the new shorter links.

New experiments processed and added to the expression browser:

Population Biology/Insecticide Resistance

10 projects have been added:

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

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

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-2017-04) is scheduled for late April.

Other known issues

Please report any problems to the helpdesk.

Release date: 
Tuesday, February 21, 2017