A parallel algorithm for the constrained multiple sequence alignment problem

@article{He2005APA,
  title={A parallel algorithm for the constrained multiple sequence alignment problem},
  author={Dan He and Abdullah N. Arslan},
  journal={Fifth IEEE Symposium on Bioinformatics and Bioengineering (BIBE'05)},
  year={2005},
  pages={258-262}
}
We propose a parallel algorithm for the constrained multiple sequence alignment (CMSA) problem that seeks an optimal multiple alignment constrained to include a given pattern. We consider the dynamic programming computations in layers indexed by the symbols of the given pattern. In each layer we compute as a potential part of an optimal alignment for the CMSA problem, shortest paths for multiple sources and multiple destinations. These shortest paths problems are independent from one another… CONTINUE READING

Citations

Publications citing this paper.
Showing 1-8 of 8 extracted citations

References

Publications referenced by this paper.
Showing 1-10 of 15 references

A fast algorithm for the Constrained Multiple Sequence Alignment problem

D. He, A. N. Arslan
Proc. 11th International Conference on Automata and Formal Languages (AFL • 2005
View 6 Excerpts
Highly Influenced

Computing the nxm Shortest Paths Efficiently

ACM Journal of Experimental Algorithmics • 2000
View 8 Excerpts
Highly Influenced

Eğecioğlu. Algorithms for the constrained common sequence problem

Ö.A.N. Arslan
Proc. Prague Stringology Conference • 2004
View 1 Excerpt

The constrained common sequence prob

Y.-T. Tsai, C. L. Lu, C. T. Yu, Y. P. Huang.
IPL • 2003

The constrained common sequence problem

Y.-T. Tsai
IPL, 88:173–176, • 2003
View 1 Excerpt

Similar Papers

Loading similar papers…