How to BLAST your Database — A Study of Stored Procedures for BLAST Searches

Abstract. Stored procedures are an important feature of all major database systems that allows to execute application logic within database servers. This paper reports on experiences to implement a popular scientific algorithm, the Basic Local Alignment Search Tool (BLAST), as stored procedures within a relational database. We implemented the un-gapped, nucleotide version of the BLAST algorithm with four different relational database engines, both commercial and open source. In an experimental evaluation, we compared our dbBLAST implementations with a standard file-based BLAST implementation from NCBI with regard to the implementation effort, runtime performance, and scalability. It shows that although our dbBLAST runs faster than the file-based BLAST program for short query sequences, all implementations lack scalability. However, the results also indicate that stored procedures require significant less development effort—both in time and space—than traditional programming approaches.