Sliding window alignment and BLAST

sbusi has asked for the wisdom of the Perl Monks concerning the following question:

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!

Comment on Sliding window alignment and BLAST

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Re: Sliding window alignment and BLAST by haukex (Archbishop) on Mar 15, 2020 at 08:54 UTC
Welcome to PerlMonks, sbusi. Note that only some of us are bioinformaticians (I am not), so if you want a broader audience for your question, it would be helpful if you could explain the terminology you're using, and/or describe your question in programming terms. See also How do I post a question effectively? and Short, Self-Contained, Correct Example: showing some short, representative sample input, the expected output corresponding to that input, the code you're currently using, and the current output including any error messages, each within `<code>` tags, will let more people take a crack at answering your question. Update: And for questions regarding matching, providing several examples instead of a single one is very helpful.	[reply] [d/l]
Re: Sliding window alignment and BLAST by johngg (Canon) on Mar 15, 2020 at 15:42 UTC
I can't help with your problem as I am not familiar with the terms you use. Have you looked at the BioPerl site here for any pointers? Update: Corrected typo, `s/us/use/` Cheers, JohnGG	[reply] [d/l]