Newsletter 2 2008-01
From VectorBase Help System
|
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.
Microarray probe drug resistance
A new detox chip has been designed by Dr. Hilary Ranson and Dr. Clare Strode, from the Liverpool School of Tropical Medicine, for a set of Aedes genes, including cytochrome P450's, glutathione S-transferase (GSTs) and carboxylesterases. The probes have been mapped to the Aedes genome and are accessible on the genome browser and in the Base expression database.
GDAV
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. GDAV also includes a DAS server so that, if the data can be mapped to one or more VectorBase genomes, these alignments can be viewed in the VectorBase genome browser.
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.
Note added after newsletter publication: configure your Anopheles gambiae genome browser to show the A. albimanus EST alignments by clicking once on this link and you should see orange features.
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.
Coming Soon
The A. gambiae and A. aegypti gene set updates are expected during the first quarter of 2008.
An assembly of the Ixodes scapularis genome has recently been completed and submitted to GenBank, and should be publicly available very soon.
We are working on generating a new Blast interface, allowing blasting against individual EST libraries or quickly selecting databases based on phylogeny.
To (un)subscribe to the newsletter, contact newsletter@vectorbase.org
VectorBase Top Tip
It is reachable from the left-hand tab of the geneview pages, under ‘gene tree info.’
The Gene Trees represent the evolutionary history of gene families. Red squares represent duplications nodes, blue squares represent speciation nodes. Clicking on an internal node gives a pop-up-menu with indications on its taxonomy and clicking on a gene gives its gene and protein IDs (linking to the cognate page), and various information. The green bars at the right of the tree are a schematic representation of the multiple alignment of the peptides made using MUSCLE. Full boxes indicate matches/mismatches, open boxes indicate gaps in the alignment.
