How Can I perform a multiple alignment with characters?

Question

[cristialf]

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

[Pierre Lindenbaum]

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.

Answer 1

[thackl]

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?

Answer 2

[Jean-Karim Heriche]

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