Release VB-2014-08

Overview

We are pleased to announce the August release of VectorBase (VB-2014-08):

  • Minor gene prediction modifications for 16 species to capture missing stop codons
  • The expression browser has been updated and is now ready to incorporate RNA-Seq differential expression data.
  • A new variation database for Anopheles stephensi SDA-500 strain.
  • Galaxy is upgraded to Beta version. The available computing resources have been extended to meet user requirements.
  • Advanced Search has been improved. Users can now bookmark the Advanced Search URLs.
  • BLAST, ClustalW, and HMMER job expiration will be enforced; Jobs ran while not logged in will expire after 14 days, jobs ran while logged in will expire after 90 days. Jobs saved under the user profile page will be saved indefinitely until the user chooses to not save them anymore.
  • BLAST default datasets and options may be saved while logged in.

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:  ).

Pre-released genomes, with mapped data but no gene predictions

Genome annotation

  • Gene predictions have been extended to find plausible stop codons (where absent) which are proximal to the end of the transcript predictions. In total 16 species have been updated:
    • Aedes aegypti AaegL3.2
    • Anopheles albimanus AalbS1.2
    • Anopheles arabiensis AaraD1.2
    • Anopheles christyi AchrA1.2
    • Anopheles darlingi AdarC3.2
    • Anopheles dirus AdirW1.2
    • Anopheles epiroticus AepiE1.2
    • Anopheles funestus AfunF1.2
    • Anopheles gambiae AgamP4.2
    • Anopheles minimus AminM1.2
    • Anopheles quadriannulatus AquaS1.2
    • Anopheles stephensi AsinS1.2
    • Biomphalaria glabrata BglaB1.2
    • Culex quinquefasciatus CpipJ2.2
    • Glossina morsitans GmorY1.4
    • Ixodes scapularis IscaW1.4

Expression Data

One new experiment has been added:

Several improvements have been made to the expression browser pages:

  • RNA-Seq experiments with biological replicates can now be incorporated into the resource. One RNA-Seq experiment for Aedes aegypti (see above) has been loaded to demonstrate this new functionality.
  • A problem with the CSV-format table downloads has been fixed, and are also more spreadsheet-friendly.
  • Probes are called probes (or probe sets or reference transcripts) and the terminology "reporter" has been phased out.
  • Now hosted on the main server farm for improved robustness and consistency.

Population Biology/Insecticide Resistance

A large batch of insecticide resistance studies has been imported from IRBase, bring the total number of projects in the population biology browser to 99.


Variation Data

New data

A new variation database has been added for the Anopheles stephensi SDA-500 strain.

Updates

Variation transcript effects were re-evaluated this release for all species.

Summary of available variation data by organism

    Reference species SNP calls (million) Indel calls (million) Last updated
    Aedes aegypti 0.28 0.004 2014-08
    Anopheles arabiensis 10.2 0.98 2014-08
    Anopheles culicifacies 9.15 0.88 2014-08
    Anopheles epiroticus 3.28 0.25 2014-08
    Anopheles funestus 12.9 0.47 2014-08
    Anopheles gambiae 7.3 1.3 2014-08
    Anopheles minimus 4.21 0.22 2014-08
    Anopheles quadriannulatus 10.1 0.89 2014-08
    Anopheles stephensi 5.8 0.57 2014-08
    Ixodes scapularis 1.19 2014-08


    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

    Ontologies

    Ontology Version Description Changes in this release
    IDODEN 1.0 Disease ontology for Dengue fever. Release of version 1.0

    Tutorials

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


    Known issues

    • The new RNA-Seq expression data appears to be missing from the expression BioMart - we will fix this before the next release if possible.

    Please report any problems to the helpdesk.

    Release date: 
    Wednesday, August 20, 2014