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Re: [ccp4bb]: Sequence Alignment



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Dr. Chris Bruns's program Sequoia was designed with precisely this in
mind.

http://bruns.homeip.net/~bruns/sequoia.html

Not only does it do protein structural alignments, it also does 
sequence/sequence alignments and has the very clever idea that a structural 
alignment is a sequence alignment is a structural alignment.   It's my 
favorite tool for aligning both sequences and structures.

And once you build a partial alignment, sequoia will never break it apart 
again (as he was a crystallographer and realized that his alignments may be 
of better quality than a sequence-only alignment).

Chris.

On Monday 18 November 2002 02:19 pm, phubbard@post.its.mcw.edu wrote:
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>
> Hello again,
>
> A related question: After performing a structure based sequence alignment
> between 2 sequences, is it possible to add another sequence of unknown
> structure (homologue) and do an alignment of that sequence without altering
> the alignment of the first 2 sequences.
>
> Thanks
>
> AGS

-- 
Christopher Putnam, Ph.D.
Ludwig Institute For Cancer Research
Cellular and Molecular Medicine East, Room 3019
9500 Gilman Drive
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cdputnam@ucsd.edu
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