Staff Publications

  • external user (warningwarning)
  • Log in as
  • language uk
Record number 531977
Title pyPaSWAS : Python-based multi-core CPU and GPU sequence alignment
Author(s) Warris, Sven; Timal, N.R.N.; Kempenaar, Marcel; Poortinga, Arne M.; Geest, Henri van de; Varbanescu, Ana L.; Nap, Jan Peter
Source PLoS One 13 (2018)1. - ISSN 1932-6203
DOI http://dx.doi.org/10.1371/journal.pone.0190279
Department(s) PRI BIOS Applied Bioinformatics
Publication type Refereed Article in a scientific journal
Publication year 2018
Abstract Background Our previously published CUDA-only application PaSWAS for Smith-Waterman (SW) sequence alignment of any type of sequence on NVIDIA-based GPUs is platform-specific and therefore adopted less than could be. The OpenCL language is supported more widely and allows use on a variety of hardware platforms. Moreover, there is a need to promote the adoption of parallel computing in bioinformatics by making its use and extension more simple through more and better application of high-level languages commonly used in bioinformatics, such as Python. Results The novel application pyPaSWAS presents the parallel SW sequence alignment code fully packed in Python. It is a generic SW implementation running on several hardware platforms with multi-core systems and/or GPUs that provides accurate sequence alignments that also can be inspected for alignment details. Additionally, pyPaSWAS support the affine gap penalty. Python libraries are used for automated system configuration, I/O and logging. This way, the Python environment will stimulate further extension and use of pyPaSWAS. Conclusions pyPaSWAS presents an easy Python-based environment for accurate and retrievable parallel SW sequence alignments on GPUs and multi-core systems. The strategy of integrating Python with high-performance parallel compute languages to create a developer- and user-friendly environment should be considered for other computationally intensive bioinformatics algorithms.
Comments
There are no comments yet. You can post the first one!
Post a comment
 
Please log in to use this service. Login as Wageningen University & Research user or guest user in upper right hand corner of this page.