JFreq (Java Word Frequencies) is a front end to Schbath’s R’MES, which is available at the R’MES website. R’MES finds the expected and actual frequencies of short nucleotide sequences, or words, using a Markov model to control for the effects of base composition and the frequencies of shorter words. Unusually frequent or infrequent occurrences of certain words may indicate biological relevance. For example, if the word “TAATTT” occurs much less frequently than expected, it might be that it performs some regulatory function, or makes the sequence vulnerable to mutation, or has some other biological function.
Dr. Chris Upton, University of Victoria, Biochemistry and Microbiology
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