Groups > comp.soft-sys.math.mathematica > #2337

Protein Sequence Alignment efficiency

From	Matteo Pendleton <znfinger@gmail.com>
Newsgroups	comp.soft-sys.math.mathematica
Subject	Protein Sequence Alignment efficiency
Date	2011-05-13 10:28 +0000
Organization	Steven M. Christensen and Associates, Inc and MathTensor, Inc.
Message-ID	<iqj14b$rg8$1@smc.vnet.net> (permalink)

Show all headers | View raw

I'm trying to do some bioinformatics work in Mathematica and I've run up
against a bit of a roadblock regarding code efficiency. I'm doing pairwise
protein sequence alignments and I've written a nice little function that
takes two sequences and returns the optimal alignment. The trouble is that
it's slow. The reason
it's slow is because changing the scoring table to the proper "BLOSUM80"
slows the operation down horribly.

Assuming:

seqa =
"QVQLVQSGAEVKKPGSSVKVSCKASGGTFSSYAISWVRQAPGQGLEWMGGIIPIFGTANYAQKFQGRVTITADESTSTAYMELSSLRSEDTAVYYCARDLETTVVTIYFDYWGQGTLVTVSS";
seqb =
"QVQLVQSGAEVKKPGASVKVSCKASGYTFTGYYMHWVRQAPGQGLEWMGRINPNSGGTNYAQKFQGRVTSTRDTSISTAYMELSRLRSDDTVVYYCARDLRRFGGVPYYFDYWGQGTLVTVSS"

While:
Timing[SequenceAlignment[seqa , seqb , MergeDifferences -> False];]

Out[1]={0., Null}

Changing the scoring table results in this:

Timing[SequenceAlignment[ seqa , seqb , SimilarityRules -> "BLOSUM80" ,
MergeDifferences -> False];]

Out[1]={0.171, Null}

..and my two strings are very similar. Is there any way to optimize the
SequenceAlignment function so that it doesn't do this or would it be better
to create a specialized alignment function based on the underlying linear
programming so that the scoring table is built in? I'd like to be able to
run millions of sequences through this function and that's not going to be
practical if I can only do 5/sec.

Thanks in advance!

Back to comp.soft-sys.math.mathematica | Previous | Next — Next in thread | Find similar | Unroll thread

Thread

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

csiph-web