Abstract

D structure alignment process has become the key focus of interest in structural bioinformatics. Yet, obtaining perfect alignment in a short execution time was not successful to this point. To overcome this problem, researchers tend to use parallel programming techniques to enhance the performance of the alignment process. In this article, we compare between two parallel programming paradigms for implementing a parallel version of the well-known pairwise alignment algorithm MatAlign. This parallel algorithm is implemented by using two common APIs for C++ parallel programming, which are OpenMP for multi-core CPUs and CUDA for multi-core GPUs. The results show that beside the significant improvement of the parallel implementation over the sequential one, it also shows that the multi-core GPU parallel programming model improves speedup over multi- core CPU programming model.

Talk to us

Join us for a 30 min session where you can share your feedback and ask us any queries you have

Schedule a call

Disclaimer: All third-party content on this website/platform is and will remain the property of their respective owners and is provided on "as is" basis without any warranties, express or implied. Use of third-party content does not indicate any affiliation, sponsorship with or endorsement by them. Any references to third-party content is to identify the corresponding services and shall be considered fair use under The CopyrightLaw.