Computational technique for improvement of the position-weight matrices for the DNA/protein binding sites

Naum I. Gershenzon, Gary D. Stormo, Ilya P. Ioshikhes

Research output: Contribution to journalArticle

63 Scopus citations

Abstract

Position-weight matrices (PWMs) are broadly used to locate transcription factor binding sites in DNA sequences. The majority of existing PWMs provide a low level of both sensitivity and specificity. We present a new computational algorithm, a modification of the Staden-Bucher approach, that improves the PWM. We applied the proposed technique on the PWM of the GC-box, binding site for Sp1. The comparison of old and new PWMs shows that the latter increase both sensitivity and specificity. The statistical parameters of GC-box distribution in promoter regions and in the human genome, as well as in each chromosome, are presented. The majority of commonly used PWMs are the 4-row mononucleotide matrices, although 16-row dinucleotide matrices are known to be more informative. The algorithm efficiently determines the 16-row matrices and preliminary results show that such matrices provide better results than 4-row matrices.

Original languageEnglish
Pages (from-to)2290-2301
Number of pages12
JournalNucleic acids research
Volume33
Issue number7
DOIs
StatePublished - Oct 20 2005

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