Question: Sequence Similarity Of Protein Alignment
1
gravatar for Bjoernsen
8.8 years ago by
Bjoernsen40
Bjoernsen40 wrote:

Hi, I would like to calculate the sequence similarity of all protein sequences of a MSA using e.g. JTT, ... The result should be an NxN matrix (N = number of sequences in the alignment).

I there a tool that I can use? I tried BioEdit and 'phylip protdist', but I get an identity matrix and a distance matrix, respectively.

similarity protein msa • 3.1k views
ADD COMMENTlink written 8.8 years ago by Bjoernsen40
1

Does setting the protdist distance model to "similarity table" give you something close to what you want?

ADD REPLYlink written 8.8 years ago by Neilfws49k

Thank you, I did not see this setting.

ADD REPLYlink written 8.8 years ago by Bjoernsen40
2
gravatar for Niek De Klein
8.8 years ago by
Niek De Klein2.5k
Netherlands
Niek De Klein2.5k wrote:

Doesn't the alignment program already give the sequence similarity? I just tested clustalW and that one does.

ADD COMMENTlink written 8.8 years ago by Niek De Klein2.5k
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