Code optimization of the subroutine to remove near identical matches in the sequence database homology search tool PSI-BLAST

Journal of Computational Biology

Volumn 17, Issue 6, 2010, Pages 819-823

  Aspnäs, Mats ^a   Mattila, Kimmo ^b   Osowski, Kristoffer ^a   Westerholm, Jan ^a  

^a ÅBO AKADEMI UNIVERSITY   (Finland)

^b CSC Scientific Computing Ltd   (Finland)

Author keywords

code optimization; gapped sequence alignment

Indexed keywords

ARTICLE; BIOLOGY; METHODOLOGY; PROTEIN DATABASE; SEQUENCE ALIGNMENT; SEQUENCE HOMOLOGY; TIME;

COMPUTATIONAL BIOLOGY; DATABASES, PROTEIN; SEQUENCE ALIGNMENT; SEQUENCE HOMOLOGY, AMINO ACID; TIME FACTORS;

EID: 77954943853     PISSN: 10665277     EISSN: None     Source Type: Journal    
DOI: 10.1089/cmb.2008.0053     Document Type: Article

References (4)

1. Altschul, S.F., Madden, T.L., Schäffer, A.A., et al. 1997. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25, 3389-3402.
2. Dongarra, J., London, K., Moore, S., et al. 2001. Using PAPI for hardware performance monitoring on Linux systems. Conf. Linux Clusters. Available at http://icl.cs.utk.edu/papi/. Accessed April 1, 2010.
3. Heger, A., Korpelainen, E., Hupponen, T., et al. 2008. PairsDB atlas of protein sequence space. Nucleic Acids Res. 36, D276-D280.
4. Kaspersky, K. 2003. Code optimization: effective memory usage. A-List. ISBN 1931769249.