PlasmoDB: the Plasmodium genome resource. A database integrating experimental and computational data

Abstract

PlasmoDB (http://PlasmoDB.org) is the official database of the Plasmodium falciparum genome sequencing consortium. This resource incorporates the recently completed P. falciparum genome sequence and annotation, as well as draft sequence and annotation emerging from other Plasmodium sequencing projects. PlasmoDB currently houses information from five parasite species and provides tools for intra- and inter-species comparisons. Sequence information is integrated with other genomic-scale data emerging from the Plasmodium research community, including gene expression analysis from EST, SAGE and microarray projects and proteomics studies. The relational schema used to build PlasmoDB, GUS (Genomics Unified Schema) employs a highly structured format to accommodate the diverse data types generated by sequence and expression projects. A variety of tools allow researchers to formulate complex, biologically-based, queries of the database. A stand-alone version of the database is also available on CD-ROM (P. falciparum GenePlot), facilitating access to the data in situations where internet access is difficult (e.g. by malaria researchers working in the field). The goal of PlasmoDB is to facilitate utilization of the vast quantities of genomic-scale data produced by the global malaria research community. The software used to develop PlasmoDB has been used to create a second Apicomplexan parasite genome database, ToxoDB (http://ToxoDB.org).

Figure 1

Composite of screen displays demonstrating features of the CD, Plasmodium GenePlot. The GenePlot home page provides access to three main tools. A graphical genome browser (A) highlights curated gene models (dark blue arrows), BLAST hits (shades of red reflect P-values), gene/coding potential predictions based on several different algorithms (PHAT, green arrows; GeneFinder, pink arrows; GlimmerM, light blue arrows; Hexamer, blue boxes), and tandem sequence repeats. Graphical views present chromosome data for individual genes and features via mouse-over; clicking on any one of these pulls up a page providing further information and evidence on all features associated with the gene. The search tool (B) performs complex searches of all genomic features and creates reports in a variety of different formats. Nucleotide sequences can be obtained from either the home page (C) or individual gene pages, using a multiple sequence retrieval tool. Some of the sequence manipulation tools available are shown in the background.