Yu-Shiang LinGPU-REMuSiC

Multiple sequence alignments with constrains has become an important problem in the computational biology. The concept of constrained sequence alignment is proposed to incorporate the biologist’s domain knowledge into sequence alignments such that the user-specified residues/segments are aligned together in the alignment results. Over the past decade, a series of constrained multiple sequence alignment tools were proposed in the literature. GPU-REMuSiC is a newest tool with the regular expression constrains and uses the graphics processing units (GPUs) with CUDA. GPU-REMuSiC can achieve 29× speedups for overall computation time by the experimental results.

Paper

• Conferences
  • Yu-Shiang Lin, Chun-Yuan Lin, Yeh-Ching Chung, “GPU-Based Cloud Service for Multiple Sequence Alignments with Regular Expression Constrains”, CloudCom, 2012.
  • Chun-Yuan Lin, Yu-Shiang Lin, Jiayi Zhou, and Chuan Yi Tang, “GPU-REMuSiC: Efficient Contrained Multiple Sequence Alignment Algorithm on Graphics Processing Units”, CTHPC, 2011.
  • Yu-Shiang Lin, Chun-Yuan Lin, Sheng-Ta Li, Joy Lee, and Chuan Yi ang, “GPU-REMuSiC: the implementation of Constrain Multiple Sequence Alignment on Graphics Processing Units”, NVIDIA GPU Computing Seminar, 2010.
• Journal
  • Che-Lun Hung, Yu-Shiang Lin, Chun-Yuan Lin, Yeh-Ching Chung, Yi-Fang Chung, “CUDA ClustalW: An efficient parallel algorithm for progressive multiple sequence alignment on Multi-GPUs”, CBAC: 58-62 (2015)
  • Chun-Yuan Lin, Yu-Shiang Lin, Efficient parallel algorithm for multiple sequence alignments with regular expression constraints on graphics processing units. IJCSE 9(1/2): 11-20 (2014)
  • Yu-Shiang Lin, Chun-Yuan Lin, Hsiao-Chieh Chi, Yeh-Ching Chung: Multiple Sequence Alignments with Regular Expression Constraints on a Cloud Service System. IJGHPC 5(3): 55-64 (2013)