Can you force two sequences to align with pairwise alignment?
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22 months ago
msening • 0

Hi, so my question is actually about finding matches between two sequences, one is fixed, the other one is from a library of sequence database. I am trying to match a sequence (A) with sequences from the library (B) and find if sequence A can be found in library B. If I can, I will mark the sequence from B that matches with A. The reason I want to ask if you can force alignments with pairwise alignment is that I am thinking to use pairwise alignment between A and sequences from B. If you can force them to align, I think it might not be a wise choice to map them with pairwise alignment. Or if I can filter out how much mismatch rate I want, it could be a good way to find the matches.

Thank you so much!

R pairwise alignment • 958 views
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You will want to use an aligner that does global alignments (keep in mind blast does local alignments). What is the size of these sequences? That may influence recommendation of the program.

Not sure why this is tagged with R.

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I was trying to do this in R, but if there is anything that can work well with it, it would be great!

I currently have 3000 sequences that I want to align against each other. The thing is that I would want to take a small chunk of one sequence and take that as A, and then align it to every sequence in library B. By doing this in R, it takes a long time to run, I am just wondering if there is any way to speed up the process.

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blast?

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I think blast might not be that useful for my purpose since it is more useful for multiple sequence alignment? Because I am looking to compare two sequences separately and move on to the next one in library B as I want to find out where the match starts in the sequence from library B (which I didn't say this in the original post). Could you elaborate more if I missed anything?

Edit: Actually you know what, I think I could do pairwise alignment multiple times and filter out those whose scores are not desirable (which I need to try out myself to see what kinds of score is not desirable). Thank you for suggesting BLAST tho!

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