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[modeller_usage] align sequences

To: modeller_usage@salilab.org
Subject: [modeller_usage] align sequences
From: rgerber2@bigred.unl.edu
Date: Tue, 21 Aug 2007 11:13:08 -0500

Hi, I have several proteins (AA sequences) that I would like tocompare for possible interactions but I do not know where they willbind. I looked at the example:

proteinA; AAAAAAAAAAAAA------------
proteinB; -------------BBBBBBBBBBBB
chimera;  AAAAAAAAAAAAABBBBBBBBBBBB

but this didn't help as I don't know where they will interact/bind.I've tried a few times to enter the sequences, but obviously amgetting error messages for incorrect format. Wondering if anyone knewhow to solve this???

Thanks for your help, rgerber

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