HAMSA: Highly Accelerated Multiple Sequence Aligner
2016
For biologists, the existence of an efficient tool for
multiple sequence alignment is essential. This work presents a
new parallel aligner called HAMSA. HAMSA is a bioinformatics
application designed for highly accelerated alignment of multiple
sequences of proteins and DNA/RNA on a multi-core cluster
system. The design of HAMSA is based on a combination of
our new optimized algorithms proposed recently of vectorization,
partitioning, and scheduling. It mainly operates on a distance
vector instead of a distance matrix. It accomplishes similarity
computations and generates the guide tree in a highly accelerated
and accurate manner. HAMSA outperforms MSAProbs with 21.9-
fold speedup, and ClustalW-MPI of 11-fold speedup. It can be
considered as an essential tool for structure prediction, protein
classification, motive finding and drug design studies
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