Newsletter 1 (Sep 2007)

Release Date: 
September, 2007
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  • Launch of the Newsletter
    Welcome to the first issue of the VectorBase Newsletter. The newsletter highlights new data sets and tool developments available from VectorBase as well as giving advanced notice of upcoming changes. The newsletter will be sent quarterly to those subscribed to the mail list.
    • New identifiers for Anopheles
      We have changed the identifiers of genes, transcripts and proteins for Anopheles gambiae to bring them in line with the VectorBase nomenclature rather than that of Ensembl. For those of you who are familiar with the Drosophila gene identifiers you'll recognise the usage of -R/P suffixes for transcripts and proteins and alternative isoforms defined by a letter (e.g. -RA, -RB, -RC etc.). A major advantage of this system is that there is now an implicit connection between a gene and it's encoded transcripts and peptides as they all share the same identifier (AGAPxxxxxx).
    • Anopheles new gene set
      A new Anopheles gene set (AgamP3.4), was released in July containing approx. 12,000 protein-coding gene predictions. Manual appraisal of predictions on chromosome arm 2L has been completed and significant volumes of community annotation have been integrated. The VectorBase nomenclature for gene identifiers (AGAPxxxxxx) is employed throughout. Further details can be found on the VectorBase A.gambiae homepage.
      Please contact the VectorBase team if you have queries about this gene set. We are especially interested to hear from researchers who think we have deleted genes or made retrograde predictions for their favourite genes.
    • Ontology for Tick anatomy
      An application ontology covering the anatomy of ticks (TADS) has been developed in collaboration with Prof. Dan Sonenshine (Old Dominion University, USA). The TADS ontology, as well as the Mosquito anatomy ontology (TGMA), are now compliant with CARO (Common Anatomy Reference Ontology). These two Controlled Vocabularies (CVs), together with two additional ones covering the disease transmission physiology that are now under development, provide the basis for the annotation of gene expression experiments.
      All VectorBase-developed ontologies are available for browsing and download.
    • Tiling array
      A. gambiae tiling array data from Halasz et al (2006) is available as a DAS track on the genome browser (ContigView). This shows expression levels in adult male and female mosquitoes for 76,782 36-mer probes designed against exons from an old Ensembl gene set (release 15) and 94,469 probes targeted at regular intervals where there were no predicted genes. Enable the DAS track using the "DAS Sources" menu in the "Detailed view" (click on the box for "Tiling Expression") and then zoom out all the way (200Kb) to see the inter-gene probes. The 36-mer probes were designed to be unique. The mapping to the current repeat-masked VectorBase assembly used Exonerate in an ungapped alignment mode where only exact matches are shown.
    • Community Annotation Submission
      VectorBase will integrate community annotations into the canonical gene sets wherever possible. We have developed a submission interface for the community using a simple Excel spreadsheet form. Submitters will need to sign up for a VectorBase User account and can then proceed to submit gene predictions, CV terms, citations and general comments. Submissions are moderated by VectorBase community representatives and displayed using DAS. All submitted annotations will be integrated into the canonical set during a subsequent gene build.
    • Coming soon
      Two new gene sets are expected by the end of this year: the mosquito Culex pippins and the body louse Pediculus humans.
    • Insecticide resistance ontology
      The insecticide resistance ontology is almost complete and will soon be available in VectorBase.
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