Efficiency of Shared-Memory Multiprocessors for a Genetic Sequence Similarity Search Algorithm
Loading...
View/Download File
Persistent link to this item
Statistics
View StatisticsJournal Title
Journal ISSN
Volume Title
Title
Efficiency of Shared-Memory Multiprocessors for a Genetic Sequence Similarity Search Algorithm
Published Date
1997
Publisher
Type
Report
Abstract
Molecular biologists who conduct large-scale genetic sequencing projects are producing an ever-increasing amount
of sequence data. GenBank, the primary repository for DNA sequence data, is doubling in size every 1.3 years.
Keeping pace with the analysis of these data is a difficult task. One of the most successful technique, for analyzing
genetic data is sequence similarity analysis-the comparison of unknown sequences against known sequences kept
in databases. As biologists gather more sequence data, sequence similarity algorithms are more and more useful, but
take longer and longer to run. BLAST is one of the most popular sequence similarity algorithms in me today, but its
running time is approximately proportional to the size of the database. Sequence similarity analysis using BLAST is
becoming a bottleneck in genetic sequence analysis. This paper analyzes the performance of BLAST on SMPs, to
improve our theoretical and practical understanding of the scalability of the algorithm. Since the database sizes are
growing faster than the improvements in processor speed we expect from Moore's law, multiprocessor architectures
appear to be the only way to meet the need for performance.
Description
Related to
Replaces
License
Series/Report Number
Funding information
Isbn identifier
Doi identifier
Previously Published Citation
Suggested citation
Chi, Ed Huai-hsin; Shoop, Elizabeth; Carlis, John; Retzel, Ernest; Riedl, John. (1997). Efficiency of Shared-Memory Multiprocessors for a Genetic Sequence Similarity Search Algorithm. Retrieved from the University Digital Conservancy, https://hdl.handle.net/11299/215348.
Content distributed via the University Digital Conservancy may be subject to additional license and use restrictions applied by the depositor. By using these files, users agree to the Terms of Use. Materials in the UDC may contain content that is disturbing and/or harmful. For more information, please see our statement on harmful content in digital repositories.