Re: how to construct multiple sequence alignment from group of pairwise alignments

It's not clear to me what you are actually asking for help with here?

Do you already know where the insertion points are and just need help with adding the dashes in the right places?

Or are you looking for an algorithm that allows you to find the insertion points?

Also, little data and/or a worked example goes a long. If you have a set of sequences--shorted to say 200/300 chars; don't post megabytes sequences) that demonstrate what you need to do, it is usually much clearer to non-bio(*) monks.

(*)Good'ol fashioned soap was good enough for my mum...{drone}... :)

Examine what is said, not who speaks -- Silence betokens consent -- Love the truth but pardon error.

"Science is about questioning the status quo. Questioning authority".

In the absence of evidence, opinion is indistinguishable from prejudice.

RIP an inspiration; A true Folk's Guy

Comment on Re: how to construct multiple sequence alignment from group of pairwise alignments

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Re^2: how to construct multiple sequence alignment from group of pairwise alignments by gudluck (Novice) on Oct 19, 2010 at 18:27 UTC
Sorry for more biological description. I have updated with very short input and output information. There are many multiple sequence alignments programs, but they all consider sequence similarity (based on physico-chemical). I mainly interested in inserting "dashes".	[reply]
Re^3: how to construct multiple sequence alignment from group of pairwise alignments by BrowserUk (Patriarch) on Oct 19, 2010 at 18:48 UTC
Are you saying you have (are given) the pairwise alignments (as strings with dashes) and all you need to produce is the "Final Multiple sequence alignment"? Also, it there a typo? `............V Ref1: CGACAAT--GCACGACAGAGGAAGCAGAACAGATATTTAGATTGCCTCTCATTTTCTCTCCC Seq1: CGACAAAAAGCACGACAGAGGAAGCAGAACAGATA-----ATTGCCTCTCATTTTC-CTCCC ............^` [download] Examine what is said, not who speaks -- Silence betokens consent -- Love the truth but pardon error. "Science is about questioning the status quo. Questioning authority". In the absence of evidence, opinion is indistinguishable from prejudice. RIP an inspiration; A true Folk's Guy	[reply] [d/l]
Re^4: how to construct multiple sequence alignment from group of pairwise alignments by gudluck (Novice) on Oct 19, 2010 at 21:09 UTC
yes need to generate MSA from the set of pairwise alignment. Thanks for informing the typo. Any how I am not looking similarity/identity of the nuceotides at various positions.	[reply]