Document Type
Article
Publication Date
2005
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.
Repository Citation
Gershenzon, N. I.,
Stormo, G. D.,
& Ioshikhes, I. P.
(2005). Computational Technique for Improvement of the Position-Weight Matrices for the DNA/Protein Binding Sites. Nucleic Acids Research, 33 (7), 2290-2301.
https://corescholar.libraries.wright.edu/physics/556
DOI
10.1093/nar/gki519
Comments
© Gershenzon, et al. 2005. Published by Oxford University Press. All rights reserved.
The following article appeared in Nucleic Acids Research 33(7), and may be found at http://nar.oxfordjournals.org/content/33/7/2290.full