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Kmer enrichment analysis
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3.2 years ago
chipolino ▴ 80

Hi everyone,

I have a list of DNA sequences in file A (fasta format) and another list of sequences in file B. There are nearly 200 sequences in file A (average length is 300 bp) and 1300 sequences in file B (average length is the same). I would like to compare these two files and get those kmers, which are enriched in sequences from file A (in comparison with the sequences in file B). How should I do it? Is there any software, with which I can do this type of analysis?

Thank you!

genome sequence • 1.2k views
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seer (program) appears to do what you need. Here is a link for the Wiki.

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Thank you very much for your response!