Multiple sequence Alignment - Perl or python algortihm (Oct/05/2006 )

Hi:

Can anybody please help with a program outline in python or in perl for multiple sequence alignment. I managed to code for sequence alignment for 2 sequences but have trouble to align more than 2 sequences.


Thanks very much

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Why why why why why would you ever want to write your own???? It requires double dynamic programming.

If I have misunderstood and you want something to do it for you use EMMA part of the EMBOSS package.

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And you have to bear in mind the time and space complexity making sure it's NOT more than O(N) squared!

Try Clustal W or T-COFFEE....they're freely available on EBI and produce quick results.

Good Luck!

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