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Bioinformatics Vol. 18 no. 9 2002
Pages 1270-1271
© 2002 Oxford University Press

Applications Note

Parallelized multiple alignment

Jens Kleinjung 1, Nigel Douglas 1 and Jaap Heringa 1,*

1 Division of Mathematical Biology, National Institute for Medical Research, Mill Hill, London NW7 1AA, UK

Received on February 15, 2002 ; revised on March 11, 2002 ; accepted on March 12, 2002

Summary: Multiple sequence alignment is a frequently used technique for analyzing sequence relationships. Compilation of large alignments is computationally expensive, but processing time can be considerably reduced when the computational load is distributed over many processors. Parallel processing functionality in the form of single-instruction multiple-data (SIMD) technology was implemented into the multiple alignment program Praline by using ‘message passing interface’ (MPI) routines. Over the alignments tested here, the parallelized program performed up to ten times faster on 25 processors compared to the single processor version.

Availability: Example program code for parallelizing pairwise alignment loops is available from http://mathbio.nimr.mrc.ac.uk/~jkleinj/tools/mpicode. The ‘message passing interface’ package (MPICH) is available from http:/www.unix.mcs.anl.gov/mpi/mpich.

Contact: jhering{at}nimr.mrc.ac.uk

Supplementary information: Praline is accessible at http://mathbio.nimr.mrc.ac.uk/praline.

* To whom correspondence should be addressed.


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