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, 31 (1), 234-6

ToxoDB: Accessing the Toxoplasma Gondii Genome

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ToxoDB: Accessing the Toxoplasma Gondii Genome

Jessica C Kissinger et al. Nucleic Acids Res.

Abstract

ToxoDB (http://ToxoDB.org) provides a genome resource for the protozoan parasite Toxoplasma gondii. Several sequencing projects devoted to T. gondii have been completed or are in progress: an EST project (http://genome.wustl.edu/est/index.php?toxoplasma=1), a BAC clone end-sequencing project (http://www.sanger.ac.uk/Projects/T_gondii/) and an 8X random shotgun genomic sequencing project (http://www.tigr.org/tdb/e2k1/tga1/). ToxoDB was designed to provide a central point of access for all available T. gondii data, and a variety of data mining tools useful for the analysis of unfinished, un-annotated draft sequence during the early phases of the genome project. In later stages, as more and different types of data become available (microarray, proteomic, SNP, QTL, etc.) the database will provide an integrated data analysis platform facilitating user-defined queries across the different data types.

Figures

Figure 1
Figure 1
Graphic illustration of the three phases of a text search. Users can select the database of BLAST results to be searched and provide up to 4 keywords joined by ‘AND’, ‘OR’ and ‘NOT’. In this case, the BLAST results for all T. gondii genomic sequences were searched for entries that contained the words, ‘surface’, ‘antigen’ and ‘Neospora’. The results summary page lists the search results for each keyword and the resulting join along with a hyperlink to the BLAST alignment containing the key words of interest. In this example, 54 hits were discovered that contained all three words. Hyperlinks in the BLAST alignment section permit users to view all BLAST hits generated by the particular draft contig (in this example TGG_1168) and connect directly to the entry for the ‘hit’ (AF132217) in the NCBI GenBank.

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