Support for BioIndexing in BLASTgres

Abstract. The ability to perform genome-wide and cross-genome data analyses can dramatically reduce the time required for new biological discoveries. This raises important issues in bioinformatics database research involving data representations and data integration. Essential biological datatypes (such as sequence locations) and tools (such as the popular BLAST sequence alignment tools) are not supported in traditional database systems, which has forced researchers to represent biological knowledge counterintuitively, and implement codes for data operations. This paper introduces BioIndexing, a conceptual infrastructure for representing and managing biological information that permits this information to be queried within a modern database system. The paper also describes an implementation — BLASTgres, an extension of the PostgreSQL database system — that provides indexable bioinformatics datatypes and joinable BLAST alignment. The sequence location datatype in BLASTgres is of specific interest, since it is indexable, essential to the sequence alignment information produced by BLAST, and pervasive in existing biological information.