GPU-based high throughput multiple sequence alignment algorithm for protein data: a preliminary study

Authors:
Rosni Abdullah;Nur'Aini Abdul Rashid;Najihah Ibrahim;Muhannad Abdul-Qader Abu-Hashem;Ibrahim Umar
Affiliations:
Universiti Sains Malaysia;Universiti Sains Malaysia;Universiti Sains Malaysia;Universiti Sains Malaysia;Universiti Sains Malaysia
Venue:
Proceedings of the ATIP/A*CRC Workshop on Accelerator Technologies for High-Performance Computing: Does Asia Lead the Way?
Year:
2012

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Abstract

Massively parallel platforms have been genuinely affordable over recent years. This breakthrough is the key factor that permits various research work that are continuously seeking for a better run-time performance of algorithms that process ever-growing amount of data. Multiple sequence alignment has been an important-yet-complex piece of algorithm in the computational sequence analysis field that naturally required to process huge sequence data. This proposed research looks into the strategies to utilise the massively parallel platforms in the quest of pursuing a better multiple sequence alignment in terms of throughput and parallel scalability. The initial strategies as well as the expected challenges are elaborated in this early phase of research. Current achievements as well as formulated future directions are discussed at the near end of this preliminary study.