Question: aligning two MSA
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gravatar for amara.jabeen86
23 months 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 • 745 views
ADD COMMENTlink modified 13 months ago by Suzanne50 • written 23 months ago by amara.jabeen860
1
gravatar for Michael Dondrup
23 months ago by
Bergen, Norway
Michael Dondrup45k 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 22 months ago • written 23 months ago by Michael Dondrup45k
1
gravatar for darcy.ab.jones
22 months ago by
darcy.ab.jones10 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 22 months ago by darcy.ab.jones10

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

ADD REPLYlink written 19 months ago by DNAngel20
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gravatar for fishgolden
22 months ago by
fishgolden360
fishgolden360 wrote:

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

ADD COMMENTlink written 22 months ago by fishgolden360
0
gravatar for Suzanne
13 months ago by
Suzanne50
Dundee, Scotland
Suzanne50 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 13 months ago by Suzanne50
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