Newsletter 12 (Nov 2011)

Release Date: 
November, 2011
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News: 
  • Genome projects approved
    VectorBase has been informed that the NIH/NIAID vector genome working group has approved two new projects. One will sequence the mite vector of scrub typhus, Leptotrombidium deliense, and provide additional genome and transcriptome sequencing of Ixodes scapularis and related ticks. The second will target genomes of 11 Simulium (black fly) species, including the major S. damnosum siblings, S. woodii, S. ochraceum and S. vittatum.
    Data: 
    • Pre-sites
      To provide faster access to upcoming genomes, we have recently introduced preliminary sites, called “pre-sites”. These contain preliminary gene annotations, transcriptome and proteome alignments and represent a snap shot of the annotation process at a given time. The rationales for presenting such data are to give more frequent updates on the annotation and to engage the community much earlier in the process. Releases are data-driven, rather than time-driven, and as such pre-sites, are updated independently of the bi-monthly release cycle. Because these data are preliminary, they are not archived and non-searchable. While we strongly encourage the community to use them, we advise not to rely on the identifiers, as these will not be tracked.
      To date, we have been providing pre-sites for two species: Rhodnius prolixus and Glossina morsitans.
      • Rhodnius prolixus pre-site
        The 0.5 gene set has been released for R. prolixus; it was built using the Ensembl annotation pipeline. It is accessible via the new Rhodnius prolixus species page. Additional features such as RNA-seq and protein similarities, ab initio predictions and EST-build genes are also available in the genome browser accessible from the species page.
      • Glossina morsitans pre-site
        The 0.5 gene set has been released for G. morsitans and is our first annotation using the MAKER pipeline (Cantarel et al., 2008), rather than the more traditional Ensembl pipeline. It is currently undergoing some analysis from the Glossina community so we only provide gene models via BLAST and the Glossina morsitans species page. We welcome any help from the community, so please contact us if you would like to be involved in the manual annotation process!
    Tools: 
    • Unified population data
      During the summer, VectorBase unveiled its “beta” population biology web resource. Our aim is to bring together all population-based studies (field or lab) into one database so that geographic, experimental, phenotypic and genotypic characteristics can be queried, analysed and visualised. For now, it is possible to browse the mosquito field samples that were originally made available in VectorBase’s IRBase and AgPopGenBase resources, along with 60 samples from the Neafsey et al. SNP-chip paper. Comments and suggestions from the community are welcome at any stage in the development of this resource.
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    Community: 
    • Meetings
      • Attending TropMed Philly?
        Visit us in the exhibits area at the ASTMH 60th Annual Meeting in Philadelphia, December 4-8, 2011. Representatives of VectorBase will be part of a shared exhibit along with several other NIH/NIAID Bioinformatics Resource Centers. VectorBase representatives will answer questions, demo VectorBase, help with queries and distribute materials.
    • Workshops
      • VectorBase workshops
        Our staff will be running a 2-day VectorBase workshop at the Liverpool School of Tropical Medicine (Liverpool, UK) in November. This event is now fully subscribed, but we invite other labs and institutes to host VectorBase workshops. You are free to select the topics you would like us to cover. If you are interested, please contact us at info@vectorbase.org for more details.
    • Networks