Question: Multiple Sequence Alignment
gravatar for Natasha
12 months ago by
Natasha30 wrote:

Hello Everyone,

I am performing multiple sequence alignment using Clustal Omega. For pairwise alignment, one can obtain the percentage similarity and percentage identity scores. When there are multiple sequences is there a way to obtain the percentage identity?

There are six sequences. I would like to obtain the percentage identity of 5 sequences with respect to one sequence.

sequencing • 340 views
ADD COMMENTlink modified 12 months ago • written 12 months ago by Natasha30

That is obtained using 5 pairwise alignments, not a multiple sequence alignment. With an MSA, you're looking for a consensus sequence. I'm guessing there are definitely tools to help you calculate % identity though, but you should really be doing multiple pairwise alignments as you don't want one non-reference sequence influencing the alignment of another.

ADD REPLYlink written 12 months ago by RamRS21k

I think water or needle from EMBOSS can report the identity.

ADD REPLYlink written 12 months ago by Sishuo Wang170
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