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

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.

SUBMITTER: Gershenzon NI

PROVIDER: S-EPMC1084321 | biostudies-literature | 2005

REPOSITORIES: biostudies-literature

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

Gershenzon Naum I NI Stormo Gary D GD Ioshikhes Ilya P IP

Nucleic acids research 20050422 7

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 stat ...[more]

PMID: 15849315

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