Architectural Refactoring for Fast and Modular Bioinformatics Sequence Search

TR Number
TR-06-20
Date
2006-09-01
Journal Title
Journal ISSN
Volume Title
Publisher
Department of Computer Science, Virginia Polytechnic Institute & State University
Abstract

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 properties. 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, adversely affecting maintainability and extensibility; an effective architectural refactoring will benefit both users and developers. This paper describes our experiences in the architectural refactoring of mpiBLAST into a modular, high-performance software package. Our evaluation of five component-oriented designs culminated in a design that enables modularity 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.

Description
Keywords
Parallel computation, Distributed computing, Bioinformatics, Software engineering
Citation