Release VB-2017-06

We are pleased to announce the June 2017 release of VectorBase (VB-2017-06):
  • Differential RNA-seq expression data added from four publications, including a study comparing Anopheles merus and An. coluzzii transcriptional responses to salinity. There is now differential expression data available for ten species.
  • Ten new population biology datasets are available, including larval habitat monitoring for Culex, Anopheles and Aedes in Chennai, India
  • In this release there were updates to the gene sets for 12 species based on community annotation, and a minor gene set update for Anopheles gambiae. The full list of species with updated gene sets in this release is Anopheles atroparvus, Anopheles christyi, Anopheles epiroticus, Anopheles gambiae, Anopheles sinensis, Glossina austeni, Glossina brevipalpis, Glossina fuscipes, Glossina morsitans, Glossina pallidipes, Glossina palpalis, Lutzomyia longipalpis and Phlebotomus papatasi.
  • Protein alignments for all species with updated gene models in this release have been regenerated. These are all-vs-all alignments between the species, which can be viewed as a track in the Genome Browser and Apollo.
  • The VectorBase REST API allowing programmatic access to data is now available for public use
  • A new beta release application - Genotype Explorer - is now available for people to try out. This application can act as a multi species viewer for genetic variation, and allows VCF file export of selected genomic regions and viewing of variants in the context of protein domains and orthologous genes. This application can be used in conjunction with the existing Sample Explorer tool for a subset of VectorBase species which will be expanded in future release releases.
  • The names for the Ixodes scapularis samples from Massachusetts (8 samples) and Wisconsin (12 samples) have been corrected to reflect the values in the BioSample database.
  • Protein domains for annotated transcriptomes have been updated to InterPro version 63.
  • In this release we have standardised on the Ensembl mart view display formats. This has resulted in some minor alterations to the mart interfaces which should not affect any functionality. If any problems are encountered please contact us.
  • We have also improved our Export Results and Export Sequences functionality. Now logged in users will be able to download an unlimited number of search results and sequences. Export Results and Export Sequences will now send the download to a background job and it will be available in the user's profile page under the Export category.
  • We have improved the functionality offered by Search. In order to not restrict our users in what they can search, we have added File Search to our search interface. To use it, click the Switch Search Type text and it will allow you to upload a file with search terms up to 5 KB in size.
  • There are tutorials and practice exercises (with answer key) for the recently launched Sample Explorer and for the new Genotype Explorer. The Apollo and Genome Browser tutorials have also been updated.
For more information please follow this link: https://www.vectorbase.org/release/release-vb-2017-06#