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Nucleic Acids Research Advance Access originally published online on December 16, 2008
Nucleic Acids Research 2009 37(3):815-824; doi:10.1093/nar/gkn981
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Nucleic Acids Research, 2009, Vol. 37, No. 3 815-824
© 2008 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Computational Biology

PSI-BLAST pseudocounts and the minimum description length principle

Stephen F. Altschul*, E. Michael Gertz, Richa Agarwala, Alejandro A. Schäffer and Yi-Kuo Yu

National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health Bethesda, MD 20894

*To whom correspondence should be addressed. Tel: +1 301 435 7803; Fax: +1 301 480 2288; Email: altschul{at}ncbi.nlm.nih.gov

Received October 15, 2008. Revised November 18, 2008. Accepted November 20, 2008.

Position specific score matrices (PSSMs) are derived from multiple sequence alignments to aid in the recognition of distant protein sequence relationships. The PSI-BLAST protein database search program derives the column scores of its PSSMs with the aid of pseudocounts, added to the observed amino acid counts in a multiple alignment column. In the absence of theory, the number of pseudocounts used has been a completely empirical parameter. This article argues that the minimum description length principle can motivate the choice of this parameter. Specifically, for realistic alignments, the principle supports the practice of using a number of pseudocounts essentially independent of alignment size. However, it also implies that more highly conserved columns should use fewer pseudocounts, increasing the inter-column contrast of the implied PSSMs. A new method for calculating pseudocounts that significantly improves PSI-BLAST's; retrieval accuracy is now employed by default.


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