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An OpenMP-based tool for finding longest common subsequence in bioinformatics

Finding the longest common subsequence (LCS) among sequences is NP-hard. This is an important problem in bioinformatics for DNA sequence alignment and pattern discovery. In this research, we propose new CPU-based parallel implementations that can provide significant advantages in terms of execution times, monetary cost, and pervasiveness in finding LCS of DNA sequences in an environment where Graphics Processing Units are not available. For general purpose use, we also make the OpenMP-based tool publicly available to end users.

The source code, used data set, and documentation is available at here

https://doi.org/10.1186/s13104-019-4256-6

Shikder, R., Thulasiraman, P., Irani, P. et al. An OpenMP-based tool for finding longest common subsequence in bioinformatics. BMC Res Notes 12, 220 (2019) doi:10.1186/s13104-019-4256-6

 

Authors

Pourang Irani

Pourang Irani

Professor
Canada Research Chair

As well as: Rayhan Shikder, Parimala Thulasiraman and Pingzhao Hu