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Using a Multiple Seq Alignment tool for pairwise alignments possible?
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4.7 years ago
nchuang • 200
@nchuang18948

Quick question. A Multiple Sequence alignment (MSA) uses dynamic programming to create alignments. Would it still be able to give a good global pairwise alignment? I tried it with TCoffee and result looked good for a query sequence with large indel and it was fast. I am just trying to get a collection of sequences aligned to a reference sequence (preferable output in fasta format). I was trying Python Pairwise2 but apparently it can't do large sequences (>3500bases) without being extremely slow.

multiple sequence alignment msa alignment • 1.2k views
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Pairwise alignment methods are built into t-coffee. See the manual.

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ok thanks I was reading their manual and it didn't specifically say so. I think Mafft stated it uses Needleman for global alignments.

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Biopython's pairwise2 has been improved regarding performance. The updated version is not merged with the main branch but you may download pairwise2.py and cpairwise2module.c from this pull request. The C file must be compiled.

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I had a lot of trouble with pairwise2. It was taking forever and I think I read somewhere that it is just too slow? I don't know if mine was the updated version.

I ended up just doing Needleman on all of them to the same reference and then used biopython to arrange them to the same positions as the reference in a numpy matrix.