TPARVADB: a public resource for housing and analyzing genomic data extracted from theileria parva and other Apicomplexan species.

Abstract

Exhaustive analysis of the newly sequenced Theileria parva genome has been hindered by absence of a T parva specific database. Such a database will enable analysis of T parva genome in a systematic framework with transcriptional data. We sought to develop TparvaDB to provide a comprehensive resource to facilitate research in development of an East Coast Fever vaccine by providing a user-friendly database of all genome and related data for T parva. TparvaDB is based on the Generic Model Organism Database (GMOD) platform. TparvaDB consists of a database of the T'parva (Muguga strain) genomic sequence integrated with Expressed Sequence Tags (EST's), Massively Parallel Signature Sequencing (MPSS) and Variable Nucleotide Transcribed Regions (VNTR's) stored in a PostgreSQL database system using the Chado schema. The database runs on a Linux platform, with several applications incorporated. These include, Gbrowse for genome browsing, Artemis and Artemis Comparison Tool (ACT) for annotation and comparative analysis of sequences and Biomart for advanced querying. TparvaDB in addition enables continuous manual multi-user online annotation of sequences in the database, supports multi species comparative analysis and offers a BLAST web query interface to unpublished local Basic Local Alignment Search Tool (BLAST) nucleotide and protein 'Lparva (Muguga) and 'Lparva (Marikebuni strain) datasets. In addition, re-annotation of the 'Lparva (Muguga strain) in TparvaDB using EST's resulted in the identification of 13 new Hypothetical Proteins and the correction of 23 Gene structures.