HAMSA: Highly Accelerated Multiple Sequence Aligner
Journal Title: International Journal of Advanced Computer Science & Applications - Year 2016, Vol 7, Issue 6
Abstract
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.
Authors and Affiliations
Naglaa Reda, Mohammed Al-Neama, Fayed Ghaleb
Keywords
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- EP ID EP112482
- DOI 10.14569/IJACSA.2016.070661
- Views 130
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