Re: [modeller_usage] align sequences

[Modeller Caretaker <modeller-care@ucsf.edu>]

rgerber2 AT bigred.unl.edu wrote:
> Hi, I have several proteins (AA sequences) that I would like to  
> compare for possible interactions but I do not know where they will  
> bind.  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 am  
> getting error messages for incorrect format.  Wondering if anyone knew  
> how to solve this???

You presumably want to do some kind of alignment. Modeller has tools to 
do this, or you can use any other sequence or structure alignment tool 
that outputs PIR format files.

	Ben Webb, Modeller Caretaker
--
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