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

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  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},
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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.