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MPI-dot2dot: A parallel tool to find DNA tandem repeats on multicore clusters
Ist Teil von
The Journal of supercomputing, 2022-02, Vol.78 (3), p.4217-4235
Ort / Verlag
New York: Springer US
Erscheinungsjahr
2022
Link zum Volltext
Quelle
SpringerNature Journals
Beschreibungen/Notizen
Tandem Repeats (TRs) are segments that occur several times in a DNA sequence, and each copy is adjacent to other. In the last few years, TRs have gained significant attention as they are thought to be related with certain human diseases. Therefore, identifying and classifying TRs have become a highly important task in bioinformatics in order to analyze their disorders and relationships with illnesses.
Dot2dot
, a tool recently developed to find TRs, provides more accurate results than the previous state-of-the-art, but it requires a long execution time even when using multiple threads. This work presents
MPI-dot2dot
, a novel version of this tool that combines MPI and OpenMP so that it can be executed in a cluster of multicore nodes and thus reduces its execution time. The performance of this new parallel implementation has been tested using different real datasets. Depending on the characteristics of the input genomes, it is able to obtain the same biological results as
Dot2dot
but more than 100 times faster on a 16-node multicore cluster (384 cores).
MPI-dot2dot
is publicly available to download from
https://sourceforge.net/projects/mpi-dot2dot
.