The statistical significance of nucleotide position-weight matrix matches.
BACKGROUND
To improve the detection of nucleotide sequence signals (e.g. promoter elements) by position-weight matrices (PWM) using the concept of statistically significant matches.


RESULTS
The Mksite program was originally developed for analyzing protein sequences. We report NMksite, a new version adapted to the processing of nucleotide sequences. NMksite creates PWM from nucleotide sequence block alignments or occurrence tables using three weight computation schemes. An original feature of NMksite is the numerical computation of the statistical significance of PWM matches. The utility of this concept is demonstrated in the context of the prediction of splice sites and promoter regions.
Claverie
J M
JM
Structural and Genetic Information Laboratory, CNRS-E.P. 91, Institute of Structural Biology and Microbiology, Marseille, France. jmc@igs.cnrs-mrs.fr
Audic
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D001483:Base Sequence; D005189:False Positive Reactions; D008432:Mathematical Computing; D010363:Pattern Recognition, Automated; D011401:Promoter Regions, Genetic; D016415:Sequence Alignment; D012984:Software; D016385:TATA Box; D014158:Transcription, Genetic