Re: Protein Sequence Alignment efficiency
- To: mathgroup at smc.vnet.net
- Subject: [mg118903] Re: Protein Sequence Alignment efficiency
- From: ZnFinger <znfinger at gmail.com>
- Date: Sun, 15 May 2011 07:04:17 -0400 (EDT)
- References: <iqj14b$rg8$1@smc.vnet.net> <iqla29$9va$1@smc.vnet.net>
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.