Question: aligning two MSA
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gravatar for amara.jabeen86
2.9 years ago by
amara.jabeen860 wrote:

hi I have to Multiple sequence alignments in clustalW format and I want to align these two MSA. how can i do it? thank you

alignment • 1.1k views
ADD COMMENTlink modified 2.1 years ago by Suzanne70 • written 2.9 years ago by amara.jabeen860
1
gravatar for Michael Dondrup
2.9 years ago by
Bergen, Norway
Michael Dondrup47k wrote:

The most straight-forward way is to run a new MSA with all the sequences from both included. Most MSA programs will either not bother about gaps, or you can tell them to de-align first.

ADD COMMENTlink modified 2.9 years ago • written 2.9 years ago by Michael Dondrup47k
1
gravatar for darcy.ab.jones
2.9 years ago by
darcy.ab.jones20 wrote:

If you'd rather keep your original MSAs you can use the profile alignment option available in T-coffee.

There's a short bit of documentation here that describes the method.

Essentially you can just run the following command in a terminal:

$ t_coffee -profile=msa01.aln,msa02.aln -outfile=combined_msas.aln

I think clustal might have a similar function but t-coffee does lots of extra bits.

Hope that helps :)

ADD COMMENTlink written 2.9 years ago by darcy.ab.jones20

Does t_coffee profile-profile alignment also add gap columns to the main profile alignment? Just curious! Thanks :)

ADD REPLYlink written 2.6 years ago by DNAngel40
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gravatar for fishgolden
2.9 years ago by
fishgolden420
fishgolden420 wrote:

MAFFT has an option "--add" for merging two MSAs, too. http://mafft.cbrc.jp/alignment/server/add.html

ADD COMMENTlink written 2.9 years ago by fishgolden420
0
gravatar for Suzanne
2.1 years ago by
Suzanne70
Dundee, Scotland
Suzanne70 wrote:

Hi, you run a range of different MSA alignments in Jalview. It allows multiple views of the same sequences that have been aligned by different methods. Jalview also has an option where sequences can be grouped and represented by single sequence. In theory it would be possible to then align these representative sequences and compare the results.

ADD COMMENTlink written 2.1 years ago by Suzanne70
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