Question

aligning two MSA

2

Entering edit mode

7.6 years ago

amara.jabeen86 ▴ 20

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 • 3.2k views

ADD COMMENT • link updated 6.8 years ago by Suzanne ▴ 100 • written 7.6 years ago by amara.jabeen86 ▴ 20

score 3 · Answer 1 · 2017-05-16

3

Entering edit mode

7.5 years ago

darcy.ab.jones ▴ 40

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 COMMENT • link 7.5 years ago by darcy.ab.jones ▴ 40

0

Entering edit mode

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

ADD REPLY • link 7.3 years ago by DNAngel ▴ 250

score 1 · Answer 2 · 2017-04-26

1

Entering edit mode

7.6 years ago

Michael 55k

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 COMMENT • link 7.5 years ago by Michael 55k

score 0 · Answer 3 · 2017-05-16

0

Entering edit mode

7.5 years ago

fishgolden ▴ 520

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

ADD COMMENT • link 7.5 years ago by fishgolden ▴ 520

score 0 · Answer 4 · 2018-02-09

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.