PlasmoDB: a functional genomic database for malaria parasites

Abstract

PlasmoDB (http://PlasmoDB.org) is a functional genomic database for Plasmodium spp. that provides a resource for data analysis and visualization in a gene-by-gene or genome-wide scale. PlasmoDB belongs to a family of genomic resources that are housed under the EuPathDB (http://EuPathDB.org) Bioinformatics Resource Center (BRC) umbrella. The latest release, PlasmoDB 5.5, contains numerous new data types from several broad categories--annotated genomes, evidence of transcription, proteomics evidence, protein function evidence, population biology and evolution. Data in PlasmoDB can be queried by selecting the data of interest from a query grid or drop down menus. Various results can then be combined with each other on the query history page. Search results can be downloaded with associated functional data and registered users can store their query history for future retrieval or analysis.

Figure 1.

Screenshots from PlasmoDB 5.5 and query workflow. (A) The top of the screenshot shows the PlasmoDB logo. On the left side are links to various sections of PlasmoDB and a point for logging in or registering as a user (not required for using the site but useful for storing search histories. The query grid is in the center and provides an access point to all searchable data in PlasmoDB. (B) This is a scheme of a workflow that a user may follow when building a set of queries. Beginning at the left, queries can be performed starting from the query grid and the results can be joined using operations available through the query history page. (C) Screen shots of a ‘key word’ search page, an example gene query history and a gene results page. Note the add column feature in the results page that allows the addition of columns with additional data and the ability to sort results.