Dear all, I am trying to align two fasta files with multiple sequences. The idea would be to use a sliding window approach, as done on this site: http://www.allermatch.org/allermatch.py/form

I want to use the same 80aa sliding window, and find all alignments with greater than 35% identity. Finally, I would like an overall identity score for the aligned sequences. I've tried BLAST, FASTA36, and DIAMOND so far. None of them have the 'sliding window' option. I even tried adjusting 'word sizes' in BLAST but no luck yet.

Any ideas on how one can pursue this? Thank you!

In reply to Sliding window alignment and BLAST by sbusi

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