This Article Full Text Full Text (PDF) Alert me when this article is cited Alert me if a correction is posted Services Similar articles in this journal Similar articles in PubMed Alert me to new issues of the journal Download to citation manager Citing Articles Citing Articles via Google Scholar Google Scholar Articles by Aynechi, T. Articles by Kuntz, I. D. Search for Related Content PubMed PubMed Citation Articles by Aynechi, T. Articles by Kuntz, I. D.

An Information Theoretic Approach to Macromolecular Modeling: I. Sequence Alignments

Tiba Aynechi ^* and Irwin D. Kuntz 

^* Graduate Group in Biophysics, and Department of Pharmaceutical Chemistry, University of California, San Francisco, California

Correspondence: Address reprint requests to Dr. Irwin D. Kuntz, Dept. of Pharmaceutical Chemistry, University of California at San Francisco, San Francisco, CA 94143-0446. Tel.: 415-476-1937; Fax: 415-502-1411; E-mail: kuntz{at}cgl.ucsf.edu.

We are interested in applying the principles of information theory to structural biology calculations. In this article, we explore the information content of an important computational procedure: sequence alignment. Using a reference state developed from exhaustive sequences, we measure alignment statistics and evaluate gap penalties based on first-principle considerations and gap distributions. We show that there are different gap penalties for different alphabet sizes and that the gap penalties can depend on the length of the sequences being aligned. In a companion article, we examine the information content of molecular force fields.