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Home | Seminars and Symposia | Past seminars/symposia: Friday, December 5, 2008

Next Generation of Selected Bioinformatics Applications: Using Massively Parallel Supercomputers

by

Carlos Sosa
Biomedical Informatics and Computational Biology
University of Minnesota
IBM

Friday, December 5, 2008
12:30 p.m. lunch
1:00 p.m. seminar

401/402 Walter Library

As part of the Biomedical Informatics and Computational Biology program at the University of Minnesota, we focus on the application of high-performance computing to different areas in Life Sciences. In this presentation we discuss some of our current work. In bioinformatics, databases for sequence search play a key role in elucidating and annotating unknown queries, such as proteins. One of the challenges that scientists face is that these databases have been growing exponentially in size. As a result, faster sequence-search algorithms as well as more sophisticated and faster computers to search these databases continue to evolve and provide new avenues to handle very time-consuming searches. Tools such the Basic Local Alignment Search Tool (BLAST) from the National Center for Biotechnology Information and the hidden Markov model-based programs such as HMMER continue to improve; however, they cannot keep up with the rate at which the database is exponentially increasing in size. Therefore, parallel implementations have emerged to address this problem. The performance of such implementations depends on a myriad of factors including algorithmic and architectural. In this study, we describe our efforts to parallelize and optimize the performance of applications such as BLAST and HMMER.