Parallelized multiple alignment

Bioinformatics. 2002 Sep;18(9):1270-1. doi: 10.1093/bioinformatics/18.9.1270.


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 The 'message passing interface' package (MPICH) is available from http:/


Supplementary information: Praline is accessible at

MeSH terms

  • Algorithms*
  • Computing Methodologies*
  • Databases, Genetic*
  • Internet
  • Sensitivity and Specificity
  • Sequence Alignment / methods*
  • Software*