HAMSA: Highly Accelerated Multiple Sequence Aligner

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

@article{Reda2016,
  title     = {HAMSA: Highly Accelerated Multiple Sequence Aligner},
  journal   = {International Journal of Advanced Computer Science and Applications},
  volume    = {7},
  number    = {6},
  year      = {2016},
  publisher = {The Science and Information Organization},
  author    = {Naglaa M. Reda and Mohammed Al-Neama and Fayed F. M. Ghaleb},
  doi       = {10.14569/IJACSA.2016.070661},
  url       = {https://doi.org/10.14569/IJACSA.2016.070661}
}