Re: Protein Sequence Alignment efficiency
- To: mathgroup at smc.vnet.net
- Subject: [mg118930] Re: Protein Sequence Alignment efficiency
- From: Armand Tamzarian <mike.honeychurch at gmail.com>
- Date: Mon, 16 May 2011 03:35:27 -0400 (EDT)
- References: iqobvk$m7j$1@smc.vnet.net
On May 15, 9:04 pm, ZnFinger <znfin... at gmail.com> wrote: > 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. OK that makes more sense. There are several biophysics and systems biology type users out there but never heard of a real world bioinformatics user so I was curious. If you're unable to get this to work in Mathematica then maybe a JLink to biojava might be the best option???