Paper Info
Title
Massively Parallel Sequence Alignment with BLAST Through Work Distribution Implemented Using PCJ Library.
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.
Year
Venue
Field
2017
ICA3PP
Sequence alignment,Computer science,Massively parallel,Parallel computing,Computational science,Throughput,Java,Scalability,Executable
DocType
Citations 
PageRank 
Conference
0
0.34
References 
Authors
4
3
Name
Order
Citations
PageRank
Marek Nowicki1123.35
Davit Bzhalava200.68
Piotr Bala310916.01