Format of multiple sequence alignment

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samkh918
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Format of multiple sequence alignment

Post by samkh918 » Fri Jun 06, 2008 5:23 am

Hello,

I was wondering how I can a multiple sequence alignment that shows the amino acid identities as dots or dashes and only shows the amino acid symbol when there is a difference.
I run the clustalW and choose different formats such as pir, phylip, gde, etc. but they show all the amino acid symbols in the alignment regardless of if they are different or identical.

Thanks for your help.

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mith
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Post by mith » Fri Jun 06, 2008 7:32 pm

What's wrong with just highlighting the blocks? Seems unnecessarily complicated to me. You might scrounge around for a perl script if this function doesn't exist.
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samkh918
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Post by samkh918 » Tue Jun 10, 2008 1:27 am

well having dashes where amino acids are the same with the consensus and showing only the "different" amino acids in an alignment provides a less complicated alignment and easier to read, that's my opinion at least.
Yes I was thinking of writing a script for it, but I have seen some programs do it in the past, I just don't remember which one.

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