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 anotherâ€¦Â CONTINUE READING