Release VB-2014-12

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Submitted by lawson on Tue, 2014-12-16 09:44

We are pleased to announce the December release of VectorBase (VB-2014-12):

  • The expression database has been "spring cleaned" to improve consistency of p-values. It also now has ontology-enhanced search.
  • Population Biology - several projects have been updated to improve data consistency and/or search.
  • Gene sets have been updated this release for: Rhodnius prolixus, Glossina austeni, Glossina brevipalpis, Glossina fuscipes and Glossina pallidipes
  • NewRNAseq sets have been added for: Lutzomyia longipalpis (x8), Glossina austeni (x2), Musca domestica (x5) and Biomphalaria glabrata (x8)
  • 146 Anopheles gambiae RNA genes that lacked external references were associated with Rfam and/or mirBase identifiers. Statistics on the coverage of pairwise alignments are now available.
  • The Blastx genomic similarity search against the combined VectorBase proteome that was initially created for use in Web Apollo is now also displayed in VectorBase. The data can be viewed as a track in the genome browser via the "protein alignments" section of the display configuration.

Genomes

VectorBase is committed to a new release every two months with all data freely available for public use based on NIH/NIAID policy. A list of these changes and the state of current versions on this date (e.g., current gene sets) can be found on the Releases section of VectorBase.

For your species of interest, click on Organism, Strain, Assembly, or Gene set to find the Genome Browser link (which looks like this:  ).

Released genomes, with gene predictions

Organism Strain Assembly Gene set Gene Count Browser
Aedes aegypti Liverpool AaegL3 AaegL3.3 17 459
Anopheles albimanus STECLA AalbS1 AalbS1.2 12 335
Anopheles arabiensis Dongola AaraD1 AaraD1.2 13 678
Anopheles atroparvus EBRO AatrE1 AatrE1.2 14 230
Anopheles christyi ACHKN1017 AchrA1 AchrA1.2 11 156
Anopheles coluzzii Mali-NIH AcolM1 AcolM1.1 14 703
Anopheles culicifacies A A-37 AculA1 AculA1.2 14 882
Anopheles darlingi Coari AdarC3 AdarC3.2 10 948
Anopheles dirus A WRAIR2 AdirW1 AdirW1.2 13 239
Anopheles epiroticus Epiroticus2 AepiE1 AepiE1.2 12 602
Anopheles farauti FAR1 AfarF1 AfarF1.2 13 703
Anopheles funestus FUMOZ AfunF1 AfunF1.2 13 756
Anopheles gambiae PEST AgamP4 AgamP4.2 13 624
Anopheles maculatus B maculatus3 AmacM1 AmacM1.2 15 046
Anopheles melas CM1001059 AmelC1 AmelC1.2 16 666
Anopheles merus MAF AmerM1 AmerM1.2 14 415
Anopheles minimus A MINIMUS1 AminM1 AminM1.2 13 128
Anopheles quadriannulatus A SANGWE AquaS1 AquaS1.2 13 857
Anopheles sinensis SINENSIS AsinS1 AsinS1.2 15 280
Anopheles sinensis China AsinC2 AsinC2.1 19 815
Anopheles stephensi SDA-500 AsteS1 AsteS1.2 13 650
Anopheles stephensi Indian AsteI2 AsteI2.2 12 350
Culex quinquefasciatus Johannesburg CpipJ2 CpipJ2.2 19 363
Glossina austeni TTRI GausT1 GausT1.1 23 384
Glossina brevipalpis IAEA GbreI1 GbreI1.1 19 916
Glossina fuscipes IAEA GfusI1 GfusI1.1 23 872
Glossina morsitans Yale GmorY1 GmorY1.4 12 962
Glossina pallidipes IAEA GpalI1 GpalI1.1 22 497
Ixodes scapularis Wikel IscaW1 IscaW1.4 20 771
Musca domestica Aabys MdomA1 MdomA1.1 15 803
Pediculus humanus USDA PhumU2 PhumU2.1 11 699
Rhodnius prolixus CDC RproC1 RproC1.3 17 244

Pre-released genomes, with mapped data and gene predictions

Organism Strain Assembly Gene set Gene Count Browser
Biomphalaria glabrata BB02 BglaB1 BglaB1.2 14 351
Lutzomyia longipalpis Jacobina LlonJ1 LlonJ1.1 10 429
Phlebotomus papatasi Israel PpapI1 PpapI1.1 12 678

Expression Data

Some older experiments within VectorBase's expression resource had issues with technical replicates (such as dye swaps) being treated the same as biological replicates. This was artificially improving p-values for those experiments. From this release onwards, only biological replicates are counted as replicates. Now if it says n=3 in the gene expression report pages, this always means that three biological replicates were analysed.

Expression data search has been improved through the use of ontology terms, particularly via the Advanced Search form. Now you can search using broad concepts (such as "alimentary") in the high (or low) conditions box, and get results items annotated with more fine-grained terms (such as "gastric caeca").

Population Biology/Insecticide Resistance

Various improvements have been made at the database level to several PopBio projects. For instance, the publications linked to Malaria Atlas Project samples are now searchable by their authors and titles (previously it was only possible to search by PubMed IDs). Also, the entire PopBio database has been updated to use the correct species names following the split of Anopheles gambiae s.s. into Anopheles coluzzii and Anopheles gambiae s.s..

Variation Data

New data

No new data sets have been added this release.

Updates

No updates to existing variation data sets have been made this release.

Summary of available variation data by organism

    Reference species SNP calls (million) Indel calls (million) Last updated
    Aedes aegypti 0.28 0.004 2014-10
    Anopheles arabiensis 10.2 0.98 2014-10
    Anopheles culicifacies 9.15 0.88 2014-10
    Anopheles epiroticus 3.28 0.25 2014-10
    Anopheles funestus 12.9 0.47 2014-10
    Anopheles gambiae 7.3 1.3 2014-10
    Anopheles minimus 4.21 0.22 2014-10
    Anopheles quadriannulatus 10.1 0.89 2014-10
    Anopheles stephensi SDA-500 5.8 0.57 2014-10
    Anopheles stephensi Indian 0.37 2014-10
    Ixodes scapularis 1.19 2014-10


    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 2014-08
    Anopheles Anopheles gambiae Anopheline mitochondrial genes 2014-08
    Culex Culex quinquefasciatus Culicine mitochondrial genes 2014-08
    Ixodidae and Argasidae Ixodes scapularis Ixodida mitochondrial genes 2014-08

    Tutorials

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


    Known issues

    • IDOMAL has not been updated yet this release. We will make these changes shortly after release.

    Please report any problems to the helpdesk.

    Release date: 
    Tuesday, December 16, 2014