VectorBase: improvements to a bioinformatics resource for invertebrate vector genomics

Abstract

VectorBase (http://www.vectorbase.org) is a NIAID-supported bioinformatics resource for invertebrate vectors of human pathogens. It hosts data for nine genomes: mosquitoes (three Anopheles gambiae genomes, Aedes aegypti and Culex quinquefasciatus), tick (Ixodes scapularis), body louse (Pediculus humanus), kissing bug (Rhodnius prolixus) and tsetse fly (Glossina morsitans). Hosted data range from genomic features and expression data to population genetics and ontologies. We describe improvements and integration of new data that expand our taxonomic coverage. Releases are bi-monthly and include the delivery of preliminary data for emerging genomes. Frequent updates of the genome browser provide VectorBase users with increasing options for visualizing their own high-throughput data. One major development is a new population biology resource for storing genomic variations, insecticide resistance data and their associated metadata. It takes advantage of improved ontologies and controlled vocabularies. Combined, these new features ensure timely release of multiple types of data in the public domain while helping overcome the bottlenecks of bioinformatics and annotation by engaging with our user community.

Figure 1.

Visualization of user data in the genome browser (image exported directly from the browser). The dark red boxes at the top represent the exons on transcript AAEL012734-RA, and the blue bar represents the contig sequence. The top track in dark grey represents the coverage plot of short-read alignments of an RNA-Seq experiment on the Aedes aegypti transcriptome. Individual read alignments extracted from a BAM-formatted file (4) are displayed underneath in light grey. The four orange tracks represent reconstructed transcript models in four replicates of the same experiment, using a custom RNA-Seq analysis procedure. The BedGraph format was used to generate the data to keep the coverage information base by base.

Figure 2.

Examples of customizable displays from the Phenovis javascript library. (A) Susceptibility status of Anopheles fluviatilis, An. annularis and An. culicifacies to insecticides in Koraput District, Orissa: [insecticide x per cent mortality]. (B) Anopheles gambiae M, S and Bamako populations [location x population] (21).