Release VB-2014-12

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
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.