![](/images/graphics-bg.png)
Position Weight Matrix, Gibbs Sampler, and the Associated Significance Tests in Motif Characterization and Prediction
Author
Source
Issue
Vol. 2012, Issue 2012 (31 Dec. 2012), pp.1-15, 15 p.
Publisher
Hindawi Publishing Corporation
Publication Date
2012-11-20
Country of Publication
Egypt
No. of Pages
15
Main Subjects
Natural & Life Sciences (Multidisciplinary)
Diseases
Abstract EN
Position weight matrix (PWM) is not only one of the most widely used bioinformatic methods, but also a key component in more advanced computational algorithms (e.g., Gibbs sampler) for characterizing and discovering motifs in nucleotide or amino acid sequences.
However, few generally applicable statistical tests are available for evaluating the significance of site patterns, PWM, and PWM scores (PWMS) of putative motifs.
Statistical significance tests of the PWM output, that is, site-specific frequencies, PWM itself, and PWMS, are in disparate sources and have never been collected in a single paper, with the consequence that many implementations of PWM do not include any significance test.
Here I review PWM-based methods used in motif characterization and prediction (including a detailed illustration of the Gibbs sampler for de novo motif discovery), present statistical and probabilistic rationales behind statistical significance tests relevant to PWM, and illustrate their application with real data.
The multiple comparison problem associated with the test of site-specific frequencies is best handled by false discovery rate methods.
The test of PWM, due to the use of pseudocounts, is best done by resampling methods.
The test of individual PWMS for each sequence segment should be based on the extreme value distribution.
American Psychological Association (APA)
Xia, Xuhua. 2012. Position Weight Matrix, Gibbs Sampler, and the Associated Significance Tests in Motif Characterization and Prediction. Scientifica،Vol. 2012, no. 2012, pp.1-15.
https://search.emarefa.net/detail/BIM-507966
Modern Language Association (MLA)
Xia, Xuhua. Position Weight Matrix, Gibbs Sampler, and the Associated Significance Tests in Motif Characterization and Prediction. Scientifica No. 2012 (2012), pp.1-15.
https://search.emarefa.net/detail/BIM-507966
American Medical Association (AMA)
Xia, Xuhua. Position Weight Matrix, Gibbs Sampler, and the Associated Significance Tests in Motif Characterization and Prediction. Scientifica. 2012. Vol. 2012, no. 2012, pp.1-15.
https://search.emarefa.net/detail/BIM-507966
Data Type
Journal Articles
Language
English
Notes
Includes bibliographical references
Record ID
BIM-507966