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Massively Parallel Sequence Alignment with BLAST Through Work Distribution Implemented Using PCJ Library

  • 2017
  • OriginalPaper
  • Chapter
Published in:
Authors
Marek Nowicki
Davit Bzhalava
Piotr Bała
Published in
Algorithms and Architectures for Parallel Processing
Publisher
Springer International Publishing

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Abstract

This article presents massively parallel execution of the BLAST algorithm on supercomputers and HPC clusters using thousands of processors. Our work is based on the optimal splitting up the set of queries running with the non-modified NCBI-BLAST package for sequence alignment. The work distribution and search management have been implemented in Java using a PCJ (Parallel Computing in Java) library. The PCJ-BLAST package is responsible for reading sequence for comparison, splitting it up and start multiple NCBI-BLAST executables. We also investigated a problem of parallel I/O and thanks to PCJ library we deliver high throughput execution of BLAST. The presented results show that using Java and PCJ library we achieved very good performance and efficiency. In result, we have significantly reduced time required for sequence analysis. We have also proved that PCJ library can be used as an efficient tool for fast development of the scalable applications.

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previous chapter A Resource Manager for Maximizing the Performance of Bioinformatics Workflows in Shared Clusters
next chapter On the Use of Binary Trees for DNA Hydroxymethylation Analysis
Title
Massively Parallel Sequence Alignment with BLAST Through Work Distribution Implemented Using PCJ Library
Authors
Marek Nowicki
Davit Bzhalava
Piotr Bała
Copyright Year
2017
Book
Algorithms and Architectures for Parallel Processing

Print ISBN: 978-3-319-65481-2

Electronic ISBN: 978-3-319-65482-9

Copyright Year: 2017

DOI
https://doi.org/10.1007/978-3-319-65482-9_36
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