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Background  Parallel computing is frequently used to speed up computationally expensive tasks in Bioinformatics.    Results  Herein, a parallel version of the multi-alignment program DIALIGN is introduced. We propose two ways of dividing the program into independent sub-routines that can be run on different processors: ( a ) pair-wise sequence alignments that are used as a first step to multiple alignment account for most of the CPU time in DIALIGN. Since alignments of different sequence pairs are completely independent of each other, they can be distributed to multiple processors without any effect on the resulting output alignments. ( b ) For alignments of large genomic sequences, we use a heuristics by splitting up sequences into sub-sequences based on a previously introduced  anchored alignment  procedure. For our test sequences, this combined approach reduces the program running time of DIALIGN by up to 97%.    Conclusions  By distributing sub-routines to multiple processors, the running time of DIALIGN can be crucially improved. With these improvements, it is possible to apply the program in large-scale genomics and proteomics projects that were previously beyond its scope.

DIALIGN P: fast pair-wise and multiple sequence alignment using parallel processors.