Question: How Can I perform a multiple alignment with characters?
0
gravatar for cristialf
5.0 years ago by
cristialf0
cristialf0 wrote:

Hi everyone, I am trying to perform a multiple alignment with characters different that aminoacids or nucleotides, e.g. (tt00000000000000000000000000000lllll00000000000T000000) ,(000K0000llll00000P00000), (000K0000lll)... I was playing with the implementation of Perl of Needleman-Wunsch algorithm, but it runs a pairwise alignment. Some suggestions? Thanks in advance

 

 

alignment • 1.1k views
ADD COMMENTlink modified 5.0 years ago by thackl2.8k • written 5.0 years ago by cristialf0

Hello cristialf!

It appears that your post has been cross-posted to another site: http://stackoverflow.com/questions/34012085/how-can-i-perform-a-multiple-alignment-with-characters

This is typically not recommended as it runs the risk of annoying people in both communities.

ADD REPLYlink written 5.0 years ago by Pierre Lindenbaum131k
2
gravatar for thackl
5.0 years ago by
thackl2.8k
MIT
thackl2.8k wrote:

Why not just convert your chars into a pseudo-protein alphabet compatible with available MSA software and back-translate afterwards? Or do you need more than 20-something supported amino acid chars?

ADD COMMENTlink written 5.0 years ago by thackl2.8k
0
gravatar for Jean-Karim Heriche
5.0 years ago by
EMBL Heidelberg, Germany
Jean-Karim Heriche23k wrote:

If you can align the sequences pairwise, then an iterative MSA algorithm like Barton-Sternberg is reasonably easy to implement.

ADD COMMENTlink written 5.0 years ago by Jean-Karim Heriche23k
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