Multiple Sequence Alignment

Question

[Natasha]

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.

[Ram]

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.

[Sishuo Wang]

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

Answer 1

[mahmud_reaz]

Analysis of structural similarity, as well as pairwise identity comparison among the amino acid sequences in multiple sequences could be perform using CLC Genomics Workbench 12.0 (QIAGEN Bioinformatics). The software has a trial version allowed to run 15 days for free.