Efficient parallel algorithm for multiple sequence alignments with regular expression constraints on graphics processing units

@article{Lin2014EfficientPA,
  title={Efficient parallel algorithm for multiple sequence alignments with regular expression constraints on graphics processing units},
  author={Chun-Yuan Lin and Yu-Shiang Lin},
  journal={IJCSE},
  year={2014},
  volume={9},
  pages={11-20}
}
Multiple sequence alignments with constraints has become an important problem in 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. RE-MuSiC is the newest tool with the regular expression… CONTINUE READING

References

Publications referenced by this paper.
Showing 1-10 of 40 references

Parallel similarity search and alignment with the dynamic programming method

  • A. R. Galper, D. L. Brutlag
  • Technique report,
  • 1990
Highly Influential
4 Excerpts

The multiple sequence alignment problem in biology

  • H. Carrillo, D. J. Lipman
  • SIAM J. Appl. Math.,
  • 1988
Highly Influential
8 Excerpts

An efficient parallel algorithm for constraint multiple sequence alignment

  • H. Tsai, C. Y. Lin, Chung, Y-C, C. Y. Tang
  • ICS
  • 2006
Highly Influential
5 Excerpts

Efficient algorithms for regular expression constrained sequence alignment

  • Chung, Y-S, C. L. Lu, C. Y. Tang
  • Lect. Notes Comput. Sci.,
  • 2006
Highly Influential
4 Excerpts

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