[Biopython] still more questions about NGS sequenbce trimming

Kiss, Csaba csaba.kiss at lanl.gov
Wed Oct 24 15:49:59 UTC 2012


Hi All!
Thanks for all your help to extract DNA sequences from sff files. Using biopython I managed to improve the sequence extraction from 3 hours to 10 minutes.
Now that I am hooked, I would like to replace mothur with some simple python functions.
Is there any function in biopython that would look for homopolymers on DNA sequences. Particularly I am looking to reject a sequence if it has more than 8 bp of stretches of any single nucleotide.

Another function I am looking for is a sliding window function along  the quality file. I could either use the fastq file or the fasta/qual file pair.

I could write these functions myself but if they are available, then it would make my life easier.
Thanks

Csaba




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