Release VB_2011-08

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 August release of VectorBase (VB-2011-08) include:

  • First announcement of the new population biology resource prototype web interface.
  • Updated Ensembl genome browser (to schema 63).

Genomes

No new genomic data has been released or updated.

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.
Glossina morsitansYale GmorY1 - Repeats, RNA-seq (via BAM files) - EST-build genes, SNAP ab initio predictions, MAKER gene predictions.

Population data

We are in the process of consolidating and enhancing VectorBase's population biology resources. We currently have a prototype population sample browser which incorporates insecticide resistance data from IRbase and karyotype and microsatellite data from labs at UCLA and UC Davis. All data and website functionality is subject to change.

Our aim is to handle all types of population data, from classical genetics to high throughput sequencing, from manipulated lab strains to "wild type" field samples. Full integration with the genomic variation data shown in the genome browser is planned. Comments and suggestions are welcome (please email the helpdesk).

Expression data

No new expression data is being released officially in VB-2011-08. However, preliminary access is available to the Anopheles gambiae circadian rhythm dataset recently published by Rund et al. via the Expression Browser Preview site. Example genes with very strong rhythmic expression are timeless and period.

A web site with specialised circadian analysis is available at http://www.nd.edu/~bioclock/

Genome browser

TThe latest version (63) of the Ensembl genome browser software has been installed at VectorBase. The main new features are:

  • Sortable tracks: In the "Region Overview" and "Region in Details", it is now possible to re-order the tracks by dragging them onto a new position.
  • New style pop up menus: the pop up menus that appears when you click on a gene, for example, have been redesigned.
  • Download as CVS: all the tables are downloadable as CVS - check out for the "CVS" icon on the top right corner of the tables.

Mitochondrial gene summaries for VectorBase genera

Mitochondrial sequences for genus Anopheles, genus Aedes, family Ixodidae, family Argasidase, genus Culex from GenBank (as of 2011-05-23) have been BLASTed against the corresponding reference mitochondrial genome, and the results have been grouped by matching genes.

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.

Known issues

None at present.

Please report any problems to the helpdesk.

Release date: 
Tuesday, August 30, 2011