PlasmoDB: the Plasmodium genome resource. An integrated database providing tools for accessing, analyzing and mapping expression and sequence data (both finished and unfinished)

Abstract

PlasmoDB (http://PlasmoDB.org) is the official database of the Plasmodium falciparum genome sequencing consortium. This resource incorporates finished and draft genome sequence data and annotation emerging from Plasmodium sequencing projects. PlasmoDB currently houses information from five parasite species and provides tools for cross-species comparisons. Sequence information is also integrated with other genomic-scale data emerging from the Plasmodium research community, including gene expression analysis from EST, SAGE and microarray projects. The relational schemas used to build PlasmoDB [Genomics Unified Schema (GUS) and RNA Abundance Database (RAD)] employ 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 version of the database is also available on CD-ROM (Plasmodium 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 enhance utilization of the vast quantities of data emerging from genome-scale projects by the global malaria research community.

Figure 1

Data for PlasmoDB is gathered from several sources and stored in relational databases, GUS and RAD, before it is integrated and processed, then served to users on the World Wide Web or on CD. Dashed lines indicate items that will be added in the future; QTL, quantitative trait loci; POP, populations studies; SNP, single nucleotide polymorphisms.

Figure 2

Composite of three screen shots demonstrating PlasmoDB features for the adenylosuccinate lyase gene, PFB0295w, located on Chr2. The official annotation from TIGR is shown in (A). A graphical view of protein features is available from the link in (B), which shows BLAST hits, predicted secondary structure, domains and motifs and signal peptides. A graphical view of the genomic sequence surrounding the gene is available from the link in (C) which shows BLASTX similarities to the non-redundant protein database (NRDB; the quality of the hit similarity is indicated by the color of the box) proteins and the location of SAGE tags, ESTs and GSSs, automated gene predictions and official annotation. Similarities to P.yoelii are shown in (D) as well as BLAST hits to the NRDB (E), predicted protein motifs (F) and predicted GO functions (G). Each part of the display is a link to further information.