Release VB-2016-10
We are pleased to announce the October 2016 release of VectorBase (VB-2016-10):
- In this release there have been updates to genes sets for multiple Anopheline species. The latest gene set updates have been derived from community supplied gene annotations for Anopheles arabiensis, Anopheles albimanus, Anopheles funestus, Anopheles gambiae, Anopheles melas, Anopheles merus and Anopheles quadriannulatus.
- Variation database samples have now been renamed after their PopBio identifiers allowing navigation between the PopBio application and the variation browser via the sample picker application
- Gene description projections have been performed one-to-many orthologs from
- Ae. aegypti to Ae. albopictus
- An. gambiae to the other Anophelines
- G. morsitans to all other Glossina species, as well as Musca domestcia and Stomoxys calcitrans
- D. melanogaster to all Glossina species, Musca domestica and Stomoxys calcitrans
- Two microarray and two RNA-seq experiments have been added to the expression browser for Ixodes scapularis, Aedes aegypti and Anopheles gambiae.
- Six insecticide resistance studies have been added to the population biology resource.
- Enabled Galaxy's Trackster visualization
- VectorBase search now provides downloads of sequences based on search results
- Improved the VectorBase Search Facet interface
- Improvements to Search Autocomplete suggestions and performance
- Three tutorials have been created for this release, the topics covered are: the use of the Expression Browser for microarrays and RNAseq, the use of RNAseq pipelines/workflows with Galaxy and the Sample picker to explore samples metadata
Genomes
Released genomes, with gene predictions
Expression data
The four new differential expression experiments are:
- Pyrethroid resistant strains (Bariami et al., 2012) (Aedes aegypti; microarray)
- Translational regulation in the midgut during falciparum infection (Mead et al., 2012) (Anopheles gambiae; RNA-seq)
- Anaplasma phagocytophilum infection in Tick cells (Villar et al., 2015) (Ixodes scapularis; RNA-seq)
- Resistant vs susceptible isofemales from Tororo (Wilding et al., 2014) (Anopheles gambiae; microarray)
See known issues section below.
Population Biology/Insecticide Resistance
Data from six insecticide resistance papers have been added:
- Knockdown resistance (kdr) mutations in Indian Anopheles culicifacies populations
- Anopheles coluzzii larval habitat and insecticide resistance in the island area of Manoka, Cameroon
- When intensity of deltamethrin resistance in Anopheles gambiae s.l. leads to loss of Long Lasting Insecticidal Nets bio-efficacy: a case study in north Cameroon
- Spatial and Temporal Trends in Insecticide Resistance among Malaria Vectors in Chad Highlight the Importance of Continual Monitoring
- Pyrethroid resistance and susceptibility to Plasmodium falciparum infection of Anopheles coluzzii populations from Yaoundé (Cameroon)
- Relationship between insecticide resistance and kdr mutations in the dengue vector Aedes aegypti in Southern China
See known issues section below.
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 | 2016-02 |
| Anopheles arabiensis | 10.2 | 0.98 | 2014-10 | 2016-10 |
| Anopheles culicifacies | 9.15 | 0.88 | 2014-10 | 2015-10 |
| Anopheles epiroticus | 3.28 | 0.25 | 2014-10 | 2015-08 |
| Anopheles farauti | 6.5 | 0.75 | 2015-06 | 2015-06 |
| Anopheles funestus | 12.9 | 0.47 | 2014-10 | 2016-10 |
| Anopheles gambiae | 7.3 | 1.3 | 2016-02 | 2016-10 |
| Anopheles melas | 3.7 | 0.41 | 2015-06 | 2016-10 |
| Anopheles merus | 6.1 | 0.53 | 2015-06 | 2016-10 |
| Anopheles minimus | 4.21 | 0.22 | 2014-10 | 2015-08 |
| Anopheles quadriannulatus | 10.1 | 0.89 | 2014-10 | 2016-10 |
| Anopheles sinensis | 5.84 | 0.41 | 2015-06 | 2015-06 |
| Anopheles stephensi SDA-500 | 5.8 | 0.57 | 2014-10 | 2015-08 |
| Anopheles stephensi Indian | 0.37 | 2014-10 | 2015-06 | |
| Ixodes scapularis | 1.78 | 2015-02 | 2015-06 |
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 and youku Channels 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 tutorials for this release are:
- Sample search and Sample picker
- Transcript data and resources for microarrays and RNAseq
- VectorBase Galaxy
Known issues
- In the Mead et al expression experiment, the Plasmodium falciparum infected and uninfected samples are unintentionally averaged together as a result of a minor curation mixup. This will be fixed in the December release.
- The Plasmodium falciparum sporozoite assays have been accidentally omitted from the database in the project imported from the Foster et al publication: "Spatial and Temporal Trends in Insecticide Resistance among Malaria Vectors in Chad Highlight the Importance of Continual Monitoring".
- Gene-averaged expression summaries for around 400 non protein-coding genes is missing in the expression resource due to a software issue. This will be fixed in the December release.
- Issues have been discovered with the 16.07 release of Galaxy. A downgrade to 16.04 is in progress. Issues may appear with Galaxy until the downgrade is stabilized.
Please report any problems to the helpdesk.
Future releases
The next VectorBase release (VB-2016-12) is scheduled for mid December.
Release date:
Thursday, October 20, 2016
