Journal of Computational Science Education: Educational Module on Genomic Sequence Alignment Using HPC

Educational Module on Genomic Sequence Alignment Using HPC

Angela B. Shiflet, George W. Shiflet, Daniel S. Couch, Pietro Hiram Guzzi, and Mario Cannataro

Volume 8, Issue 1 (February 2017), pp. 7–11

https://doi.org/10.22369/issn.2153-4136/8/1/2

BibTeX

@article{jocse-8-1-2,
  author={Angela B. Shiflet and George W. Shiflet and Daniel S. Couch and Pietro Hiram Guzzi and Mario Cannataro},
  title={Educational Module on Genomic Sequence Alignment Using HPC},
  journal={The Journal of Computational Science Education},
  year=2017,
  month=feb,
  volume=8,
  issue=1,
  pages={7--11},
  doi={https://doi.org/10.22369/issn.2153-4136/8/1/2}
}

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"Aligning SequencesSequentially and Concurrently," an educational computational science module by the authors and available online, develops a sequential algorithm to determine the highest similarity score and the alignments that yield this score for two DNA sequences. Moreover, the module considers several approaches to parallelization and speedup. Besides a serial implementation in C, a parallel program in C/MPI is available. This paper describes the module and details experiences using the material in a bioinformatics course at University "Magna Graecia" of Catanzaro, Italy. Besides being appropriate for such a course, the module can provide a meaningful application for a high performance computing or a data structures class.