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Bioinformatics Advance Access published online on March 12, 2008
Bioinformatics, doi:10.1093/bioinformatics/btn097
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© The Author (2008). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

Optimizing the size of the sequence profiles to increase the accuracy of protein sequence alignments generated by profile-profile algorithms

Aleksandar Poleksic 1,* and Mark Fienup 1

1Department of Computer Science, University of Northern Iowa, Cedar Falls, IA, 50614

*To whom correspondence should be addressed. Prof. Aleksandar Poleksic, E-mail: poleksic{at}cs.uni.edu


  Abstract

Motivation: Profile-based protein homology detection algorithms are valuable tools in genome annotation and protein classification. By utilizing information present in the sequences of homologous proteins, profile-based methods are often able to detect extremely weak relationships between protein sequences, as evidenced by the large scale benchmarking experiments such as CASP and LiveBench.

Results: We study the relationship between the sensitivity of a profile-profile method and the size of the sequence profile, which is defined as the average number of different residue types observed at the profile’s positions. We also demonstrate that improvements in the sensitivity of a profile-profile method can be made by incorporating a profile dependent scoring scheme, such as position specific background frequencies. The techniques presented in this paper are implemented in an alignment algorithm UNI-FOLD. When tested against other well established methods for fold recognition, UNI-FOLD shows increased sensitivity and specificity in detecting remote relationships between protein sequences.

Availability: UNI-FOLD Web server can be accessed at http://blackhawk.cs.uni.edu

Contact: poleksic{at}cs.uni.edu

Associate Editor: Prof. Burkhard Rost

Received on January 9, 2008; revised on March 3, 2008; accepted on March 7, 2008

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