Groups | Search | Server Info | Keyboard shortcuts | Login | Register [http] [https] [nntp] [nntps]

Groups > comp.soft-sys.math.mathematica > #2365

Re: Protein Sequence Alignment efficiency

Show all headers | View raw

On May 13, 8:28 pm, Matteo Pendleton <znfin...@gmail.com> wrote:
> 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!


Out of curiosity what led you to try to use Mathematica for this task?

Mike

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