Newsletter 2 (Jan 2008)

Release Date: 
January, 2008
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News: 
  • Culex pipiens The genome of the mosquito Culex pipiens, vector of the West Nile Virus, has been sequenced and annotated and is now available at VectorBase. It complements the existing genomes of Anopheles gambiae and Aedes aegypti, completing the "mosquito triad", with one representative in each of the three main mosquito families being sequenced (Anopheline, Aedine and Culicine). The genome has been sequenced jointly by the Broad Institute and J. Craig Venter Institute (JCVI), and funded by NIAID. The shotgun sequencing was completed at the end of June 2006 and a first assembly of the 3,171 supercontigs, CpipJ1, has been produced by The Broad Institute using their whole genome assembly package ARACHNE. The 540 Mb assembly has been jointly annotated by the Broad Institute, JCVI and VectorBase. A total of 20,316 protein-coding genes were identified. Fasta files of the gene, transcript and protein sequences are available in the download section of VectorBase and the genome can be browse via our genome browser, with comparative data linking the three mosquito genomes.
Data: 
Tools: 
  • Genome De-linked Annotation Viewer
    As a result of feedback from within the community, we recognised a need for a method to disseminate annotation for species with data (e.g. EST sets) that lack genomic sequence. To meet this need, VectorBase has developed GDAV (Genome De-linked Annotation Viewer) - a lightweight web application which provides display and search facilities for sequence and text-based annotation.
    The first use of GDAV has been to publish the annotation of around 5,000 Anopheles albimanus ESTs at the Institute of Public Health, Mexico. This GDAV instance contains InterPro annotations and alignments to A. gambiae, A. aegypti and D. melanogaster.
  • HMMER Tools
    Providing multiple sequence alignments, the HMMER tools (HMMER Build & HMMER Search) create a probabilistic model that is then used to search the VectorBase databases. HMMER is similar to BLAST but is less likely to be affected by noise due to conservative or semi-conservative substitutions.
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