GiardiaDB and TrichDB: integrated genomic resources for the eukaryotic protist pathogens Giardia lamblia and Trichomonas vaginalis

Abstract

GiardiaDB (http://GiardiaDB.org) and TrichDB (http://TrichDB.org) house the genome databases for Giardia lamblia and Trichomonas vaginalis, respectively, and represent the latest additions to the EuPathDB (http://EuPathDB.org) family of functional genomic databases. GiardiaDB and TrichDB employ the same framework as other EuPathDB sites (CryptoDB, PlasmoDB and ToxoDB), supporting fully integrated and searchable databases. Genomic-scale data available via these resources may be queried based on BLAST searches, annotation keywords and gene ID searches, GO terms, sequence motifs and other protein characteristics. Functional queries may also be formulated, based on transcript and protein expression data from a variety of platforms. Phylogenetic relationships may also be interrogated. The ability to combine the results from independent queries, and to store queries and query results for future use facilitates complex, genome-wide mining of functional genomic data.

Figure 1.

Screenshots of queries available through GiardiaDB (similar queries are also available for TrichDB). (A) starting with the home page of GiardiaDB (or TrichDB), users may access ‘Queries & Tools’ via the green navigation bar. (B) Highlighted queries focus on EST evidence (black), microarray expression (orange) or GO terms (green), yielding results shown in a ‘Gene Results’ page (C), which can be organized by the addition (or deletion) of data columns (menu inset), or sorted based on any column of interest. Hot-links provide direct access to individual gene record pages of interest. (D) The results obtained from any queries run by the user are stored under ‘Query History’ (green navigation bar), which may be combined using Boolean operations available. (E) a sample gene record page, corresponding to the Multidrug Resistance Protein B (GL50803_17305), identified through the Boolean combination shown in (D). Gene record pages may be accessed from several locations, including the Gene Result page C (by clicking on gene IDs of interest), by entering the gene ID on the home page (A, gray arrow), or by clicking on gene glyphs shown in genomic context at the top the gene record page (permits sequential ‘walking’ along the chromosome to neighboring genes, or more distant genes when viewing within the Genome Browser).