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I have a DNA sequence of a protein and around 1200 zinc finger target sequences. These zinc finger target sequences are 9 bp long, resulting in BLASTn not finding them in the sequence. Needleman-Wunsch does find them, however, I can only search/align the DNA protein sequence with 1 zinc finger at a time. Is there a way to do this simultaneous (serial or parallel, computational time is not a big problem) for all 1200 zinc fingers and have the result in a table as with BLAST?

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    $\begingroup$ Could you clarify please. 1. Do you want a multiple sequence alignment with your protein and 1200 zinc fingers all aligned, or do you want to find out which of the 1200 zinc fingers align? 2. Do you really mean zinc fingers? This term is usually employed for the protein motif that binds zinc through non-adjacent Cys and His residues. A 9bp sequence could only encode three amino acids. $\endgroup$
    – David
    Dec 23, 2021 at 18:07
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    $\begingroup$ Also: by "Needleman-Wunsch" what do you mean? Are you using a specific software tool? $\endgroup$ Dec 23, 2021 at 22:22
  • $\begingroup$ Welcome to Biology.SE. I’m voting to close this question because it lacks clarity and doesn't seem to be about a biological mechanism or process. This question might be a better fit for Bioinformatics, but please do not crosspost, instead request migration after reading that sites help. Please take the tour and then go through the help center pages starting with How to Ask questions effectively on this site for details. $\endgroup$
    – tyersome
    Dec 23, 2021 at 22:27
  • $\begingroup$ @MaximilianPress — NW is a specific algorithm for global pairwise alignment and has an entry in Wikipedia, as I imagine you are aware. I therefore don’t understand what you are getting at in your comment, as the particular implementations wouldn’t seem relevant. And, of course, it is the wrong tool here — Smith-Waterman local alignment is more appropriate. $\endgroup$
    – David
    Dec 24, 2021 at 9:14
  • $\begingroup$ @David different software can have different parameters which control execution. Possibly a simple change of parameters would get the OP what they wanted out of "NW", depending on the tool, their inputs, etc. It does not seem to be an algorithmic problem as many algorithms might get them more or less the right answer (SW being another example that might work as you say, or my simple-minded suggestion below). Rather, they don't like the outputs and mode of execution of the tools they're using. $\endgroup$ Jan 1, 2022 at 21:28

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(I assume that by "DNA protein" you mean "coding DNA".)

"I can only search/align the sequence with 1 zinc finger at a time" - does this mean that you have not found out a way to do so, or that you desire to proceed in this fashion? I think that it is the first, based on the title of your question, but it is not at all clear what you are looking to do.

If you want to locate specific 9bp motifs in your sequence, then I can suggest this small piece of code that I wrote that looks for exact matches of specific sequences, that outputs a BLAST-like table. It is slow relative to BLASTN but it does not use the short-match-ignoring heuristics that BLASTN relies upon so it may be helpful.

The code was written in response to this bioinformatics SE question, which seems somewhat similar to your question here.

Note that you will have to input each expected 9bp query against the reference sequence in the form of a FASTA file.

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  • $\begingroup$ So, I shot myself in the foot a bit by posting this question before the holidays. Sorry for not responding in a better fashion. Thank you for your answer, that will certainly help me further! $\endgroup$
    – honhon
    Jan 3, 2022 at 10:30

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