Sciweavers

Share
BMCBI
2004

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

8 years 11 months ago
DIALIGN P: Fast pair-wise and multiple sequence alignment using parallel processors
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 tim...
Martin Schmollinger, Kay Nieselt, Michael Kaufmann
Added 16 Dec 2010
Updated 16 Dec 2010
Type Journal
Year 2004
Where BMCBI
Authors Martin Schmollinger, Kay Nieselt, Michael Kaufmann, Burkhard Morgenstern
Comments (0)
books