Groups > comp.soft-sys.math.mathematica > #2389

Re: Protein Sequence Alignment efficiency

From	ZnFinger <znfinger@gmail.com>
Newsgroups	comp.soft-sys.math.mathematica
Subject	Re: Protein Sequence Alignment efficiency
Date	2011-05-15 11:04 +0000
Organization	Steven M. Christensen and Associates, Inc and MathTensor, Inc.
Message-ID	<iqobvk$m7j$1@smc.vnet.net> (permalink)
References	<iqj14b$rg8$1@smc.vnet.net> <iqla29$9va$1@smc.vnet.net>

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I'm creating a generalized method for developing biologic therapeutic
agents that is heavily dependent on some systems biology requiring a
lot of differential calculus, network analysis, some manipulation of
crystal structures and some protein sequence space operations. All of
those things I have in place from earlier work (and they function
quickly even with lots of sequences/structures) but part of the front
end of the software is dependent on producing i -> j SW alignment
pairs from a large sequence library. There's an additional
functionality I'd like to add on later that requires dynamically
updating that set of sequences, so this ability to do quick pairwise
alignments is rather critical and I'd rather not have to resort to
introducing scripts from other languages if I don't have to,
particularly when Mathematica should have the ability to perform this
operation quickly.

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Protein Sequence Alignment efficiency Matteo Pendleton <znfinger@gmail.com> - 2011-05-13 10:28 +0000
  Re: Protein Sequence Alignment efficiency Armand Tamzarian <mike.honeychurch@gmail.com> - 2011-05-14 07:13 +0000
    Re: Protein Sequence Alignment efficiency ZnFinger <znfinger@gmail.com> - 2011-05-15 11:04 +0000

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