newsletter_2011

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Newsletter 11 (May 2011)

Release Date: 
May, 2011
News: 
  • Funding Opportunity
    The NIAID-funded VectorBase invites research investigations called Driving Biological Projects (DBPs) from organizations housing experimental laboratories having expertise and knowledge in working with arthropod vectors of human pathogens. We anticipate making two awards of up to $600K each by April 1, 2012. A two page Letter of Intent (LOI) is due August 1, 2011. Full proposals will be solicited by invitation only, with a deadline of November 1, 2011. See the full solicitation from the VectorBase site and send questions to vector@nd.edu.
  • Anopheles Genomes Cluster
    Samples are now in sequencing at the Broad Institute for the NHGRI/NIAID-supported project, “Genome Analysis of Vectorial Capacity in Major Anopheles Vectors of Malaria Parasites”. VectorBase looks forward to working together with the Broad and members of the vector community to process and host these new genomes and their meta-data. Please visit VectorBase often for project information, updates, and data as they become available.
Data: 
  • Rhodnius prolixus
    An early pre-release of the Rhodnius prolixus genome is available. This annotation includes: repeat masking, ESTs and RNA-seq transcriptome alignments, UniProt peptide alignments, Genscan based gene models and an transcriptome derived geneset. Further data sets will be added in the coming months with the expected pre-release of the first genebuild for the June release.
  • Glossina morsitans
    The genome of the Tsetse fly, Glossina morsitans morsitans, has been sequenced and assembled by the Wellcome Trust Sanger Institute. A pre-release of the assembly will be available in the June release. Like the Rhodnius pre-release this will contain alignments of transcriptome and peptide data and ab initio gene predictions.
Tools: 
  • Next-generation RNA-seq
    VectorBase now contains next-generation transcriptome sequence data sets (RNA-seq). Over the past few releases we have added data from 9 Anopheline species available for querying via the BLAST server and as data tracks served to the Anopheles gambiae browser via DAS. Further, the genome browser is now capable of displaying community members’ own indexed BAM files for all species.

    As more data sets become available VectorBase will continue to make these available to the community. A major update for Aedes aegypti is due for the June release including 1.3 M Roche 454 reads and 41 M Illumina reads from the Short Read Archive (SRA). We encourage our communities to contact us early to discuss visualization of newer generation sequencing data sets through VectorBase including resequencing data.

Community: 
  • Meetings
    • 7th Annual BioMalPar Conference, Biology and Pathology of the Malaria Parasite. EMBL Heidelberg, Germany 16-18th May 2011
    • 5th Annual Arthropod Genomics Symposium Arthropod Genomics 2011: Exploring Diversity, Relating Similarity. Kansas City, USA, June 9 - 12, 2011
    • Fifth International Meeting on "Molecular and Population Biology of Mosquitoes and Other Disease Vectors". Kolymbari, Crete, Greece, 24-30 July 2011
    • Workshops
    • Networks
Contact us: 

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Top tip: 
  • Variant Effect Predictor
    Did you know you can predict the effect of variants within the vector genomes? A variant effect predictor is available through the ’Manage your data’ button found in the left hand navigation menu of the genome browser. Users can upload a text file containing the variation data in a tab-separated format (chromosome, start, end, allele, strand) and the predictor will return the consequence of this variation with information about the affected gene and transcript, any amino acid changes and whether this variation is currently in the database. Full documentation relating to both input and output file formats can be found at http://www.vectorbase.org/info/website/upload/var.html
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    Newsletter 12 (Nov 2011)

    Release Date: 
    November, 2011
    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.
      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
      Contact us: 

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      Top tip: 

      VectorBase Top Tip : Switch on a genome browser track via email It is now possible to send a link via email which will turn on a specified track in the recipient’s genome browser. This saves explaining to your colleagues and collaborators how to “Configure this page...”. Simply mouse-over the track name and then the chain-link icon in the popup. Then copy the URL (right mouse-click menu in most web browsers). Here is the (shortened) link from the graphic below (goo.gl/WL1pf) to prove that it works.

      Updated on February 2014: The above tip corresponds to an older version of VectorBase genome browser. In the current version you can click on the share icon highlighted below.

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