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Bioinformatics Advance Access published online on October 27, 2004
Bioinformatics, doi:10.1093/bioinformatics/bti070
Bioinformatics © Oxford University Press 2004; all rights reserved
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Received June 14, 2004
Revised August 6, 2004
Accepted September 13, 2004

Article

The construction of amino acid substitution matrices for the comparison of proteins with non-standard compositions

Yi-Kuo Yu 1 and Stephen F. Altschul 1*

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

* To whom correspondence should be addressed.
Stephen F. Altschul, E-mail: altschul{at}ncbi.nlm.nih.gov


  Abstract

Motivation: Amino acid substitution matrices play a central role in protein alignment methods. Standard log-odds matrices, such as those of the PAM and BLOSUM series, are constructed from large sets protein alignments having implicit background amino acid frequencies. However, these matrices frequently are used to compare proteins with markedly different amino acid ompositions, such as transmembrane proteins or proteins from organisms with strongly biased nucleotide compositions. It has been argued elsewhere that standard matrices are not ideal for such comparisons and, furthermore, a rationale has been presented for transforming a standard matrix for use in a non-standard compositional context.

Results: This paper presents the mathematical details underlying the compositional adjustment of amino acid or DNA substitution matrices.

Availability: Programs implementing the methods described are available from the authors upon request.


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