Architectural Refactoring for Fast and Modular Bioinformatics Sequence Search

Bioinformaticists use the Basic Local Alignment Search Tool (BLAST) to characterize an unknown sequence by comparing it against a database of known sequences, thus detecting evolutionary relationships and biological proper-ties. mpiBLAST is a widely-used, high-performance, open-source parallelization of BLAST that runs on a computer cluster delivering super-linear speedups. However, the Achilles heel of mpiBLAST is its lack of modularity, ad-versely affecting maintainability and extensibility; an effec-tive architectural refactoring will benefit both users and de-velopers. This paper describes our experiences in the architectural refactoring of mpiBLAST into amodular, high-performance software package. Our evaluation of five component-oriented designs culminated in a design that enables mod-ularity while retaining high-performance. Furthermore, we achieved this refactoring effectively and efficiently using eXtreme Programming techniques. These experiences will be of value to software engineers faced with the challenge of creating maintainable and extensible, high-performance, bioinformatics software. 1