HAMSA: Highly Accelerated Multiple Sequence Aligner
| Autor: | Mohammed W. Al-Neama, Fayed F. M. Ghaleb, Naglaa M. Reda |
|---|---|
| Rok vydání: | 2016 |
| Předmět: |
0301 basic medicine
Sequence Multiple sequence alignment Speedup General Computer Science Computer science RNA 03 medical and health sciences chemistry.chemical_compound Tree (data structure) ComputingMethodologies_PATTERNRECOGNITION 030104 developmental biology chemistry Distance matrix Vectorization (mathematics) Algorithm DNA |
| Zdroj: | International Journal of Advanced Computer Science and Applications. 7 |
| ISSN: | 2156-5570 2158-107X |
| DOI: | 10.14569/ijacsa.2016.070661 |
| Popis: | 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 |
| Databáze: | OpenAIRE |
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