Most frequent substring of a given length
Is there anything in Biopython which could give the most frequently occurring substring of a given length from a sequence read?
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venu
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luca.pamparana •
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luca.pamparana •
2 answers
If language doesn't matter, you can use this bash (includes a perl script) script. I did not update this from a long time but it works pretty well. You can give the k-mer length of your interest. Output will be as follows or you can modify according to your needs.
TAACCCTAAC 23
AACCCTAACC 21
ACCCTAACCC 20
CCCTAACCCT 20
CCTAACCCTA 20
CTAACCCTAA 18
TAACCCTAAC 18
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How about a k-mer counter, like khmer (not Biopython, but C++ with Python wrapper)?
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harold.smith.tarheel
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