Release VB_2011-04

Note, this is legacy information that refers to an older version of the VectorBase website.
Hyperlinks have been removed and URLs may no longer be valid.

Overview

Highlights of the April release of VectorBase (VB-2011-04) include:

  • New microarray expression data for Culex quinquefasciatus and Aedes aegypti
  • Updated mass spec. peptides for Anopheles gambiae available via DAS and simple browsing interface
  • Anopheles funestus RNAseq contigs available for BLAST and browsing and search
  • GTF file format for use in tophat/cufflinks analysis of RNA-seq data available for download from all species.

Genomes

Fully released genomes, with gene predictions

Species Assembly Gene set GenBank WGS
Aedes aegypti Liverpool AaegL1 AaegL1.2 AAGE02000000
Anopheles gambiae PEST AgamP3 AgamP3.6 AAAB01000000
Culex quinquefasciatus JHB CpipJ1 CpipJ1.2 AAWU01000000
Ixodes scapularis Wikel IscaW1 IscaW1.1 ABJB01000000
Pediculus humanus USDA PhumU1 PhumU1.2 AAZO01000000

Pre-released genomes, with mapped data but no gene predictions

Species Assembly GenBank WGS Data available
Anopheles gambiae M AgamM1 ABKP00000000 Repeats, ESTs
Anopheles gambiae S AgamS1 ABKQ00000000 Repeats, ESTs
Rhodnius prolixus CDC RproC1 ACPB00000000 Repeats, ESTs, RNA-seq and protein similarities - GenScan ab initio predictions and EST-build genes.

Expression data

Three microarray experiments have been added, from two publications:

  • Permethrin resistant Culex quinquefasciatus strain comparison (Komagata et al., 2010)
  • Blood meal timecourse in Aedes aegypti (Dissanayake et al., 2010)
  • Male vs. female comparison in Aedes aegypti(Dissanayake et al., 2010)

The Aedes aegypti SINV infection experiment has been removed due to data processing issues. However, raw and processed data files for this experiment are available at ArrayExpress, and its array probes will remain available in VectorBase's genome browser.

The Expression Biomart has been updated to reflect the changes and additions. The Anopheles gambiae Expression Map and download files remain unchanged (no new data for this organism this release).

Genome browser

An updated Anopheles gambiae mass spectrometry proteomics dataset courtesy of the Pandey lab (JHU) has been incorporated into the genome browser. There were no upgrades to the genome browser software for this release. We encourage you to report any issues to the VectorBase helpdesk.

Download area

  • Update of all EST transcriptome files to ENA release 106 (Dec 2010). Sequences are available both as raw fasta and clipped to remove poly A/T runs.
  • Minor corrections to the fasta headers for the proteome and transcriptome files for all species.
  • Corrections to better handle UTR annotations in GFF3 files for all species.
  • First release of GTF files suitable for use in tophat/cufflinks analysis for all species.

Mitochondrial gene summaries for VectorBase genera

Mitochondrial sequences for genus Anopheles, genus Aedes, family Ixodidae, family Argasidase, genus Culex from GenBank (as of 2011-03-23) have been BLASTed against the corresponding reference mitochondrial genome, and the results have been grouped by matching genes.

Links to Mitochondrial data for the 4 main genera are presented below for convenience.

Genus/genera Reference species Mitochondrial gene resource Last updated
Aedes Aedes aegypti http://aaegypti.vectorbase.org/SequenceData/Mitochondria/ 2011-01-20
Anopheles Anopheles gambiae http://agambiae.vectorbase.org/SequenceData/Mitochondria/ 2011-01-20
Culex Culex quinquefasciatus http://cquinquefasciatus.vectorbase.org/SequenceData/Mitochondria/ 2011-01-20
Ixodidae and Argasidae Ixodes scapularis http://iscapularis.vectorbase.org/SequenceData/Mitochondria/ 2011-01-20

Ontologies

VectorBase supports four ontologies developed by IMBB with members of the research community. These are available for browsing and download.

There are no updates for this release.

Ontology Version Description
MIRO 1.8 An ontology to describe mosquito populations, methods and mechanisms that are used to identify/monitor insecticide resistance.
TGMA 1.1 An ontology to describe the anatomy of mosquitoes.
TADS 1.2 An ontology to describe the anatomy of ticks.
IDOMAL 1.2 An ontology to describe all aspects of malaria. Clinical data, epidemiological data, biological data concerning vertebrate hosts, vectors and parasites as well as interventions and attempts to control the disease.

Tools

The BLAST user interface has been beautified via HTML5 and is visible with Chrome, Safari, and the newest version of Firefox. As well as adding Rhodnius prolixus data to the BLAST facility at VectorBase, we have made it easier to search the eight Anopheline RNAseq datasets. Simply select "Other organisms" in the main BLAST menu. Results are now linked through to sequence report pages.

Known issues

Please check the VectorBase Twitter page for news on these few remaining issues.

Genome browser: Gene & Transcript pages for GenScan predictions

The Gene and Transcript pages for the GenScan predictions are not activated. This is due to the way the GenScan data are stored in the database. This issue has been addressed and will be corrected for next release.

CV Search

The Controlled Vocabulary (CV) search pages are currently not working. Selecting an ontology to browse will not initiate a session. We are working on this issue and hope to re-instate the browser as soon as possible.

Please report any problems to the helpdesk.

Release date: 
Saturday, April 30, 2011