Encyclopedia of Systems Biology

2013 Edition
| Editors: Werner Dubitzky, Olaf Wolkenhauer, Kwang-Hyun Cho, Hiroki Yokota

Position Weight Matrices

Reference work entry
DOI: https://doi.org/10.1007/978-1-4419-9863-7_439



A position weight matrix (PWM) is a commonly used representation of motifs (patterns) in biological sequences (Ben-Gal et al. 2005). In a position weight matrix, each row corresponds to one symbol of the alphabet, e.g., amino acids or nucleic acids, and each column corresponds to one position in the pattern. The score assigned by a PWM corresponding to a substring \( S{ = }\left( {{S_j}} \right)_{{j = 1}}^N \)

This is a preview of subscription content, log in to check access.


  1. Beckstette M et al (2006) Fast index based algorithms and software for matching position specific scoring matrices. BMC Bioinformatics 7:389PubMedGoogle Scholar
  2. Ben-Gal I et al (2005) Identification of transcription factor binding sites with variable-order Bayesian networks. Bioinformatics 21(11):2657–2666PubMedGoogle Scholar
  3. Kel AE et al (2003) MATCH: a tool for searching transcription factor binding sites in DNA sequences. Nucleic Acids Res 31(13):3576–3579PubMedGoogle Scholar

Copyright information

© Springer Science+Business Media, LLC 2013

Authors and Affiliations

  1. 1.Institute of Systems BiologyShanghai UniversityShanghaiChina