PMID- 30004240
OWN - NLM
STAT- MEDLINE
DCOM- 20191023
LR  - 20191023
IS  - 1557-8666 (Electronic)
IS  - 1066-5277 (Linking)
VI  - 25
IP  - 8
DP  - 2018 Aug
TI  - Massively Parallel Implementation of Sequence Alignment with Basic Local 
      Alignment Search Tool Using Parallel Computing in Java Library.
PG  - 871-881
LID - 10.1089/cmb.2018.0079 [doi]
AB  - Basic Local Alignment Search Tool (BLAST) is an essential algorithm that 
      researchers use for sequence alignment analysis. The National Center for 
      Biotechnology Information (NCBI)-BLAST application is the most popular 
      implementation of the BLAST algorithm. It can run on a single multithreading 
      node. However, the volume of nucleotide and protein data is fast growing, making 
      single node insufficient. It is more and more important to develop 
      high-performance computing solutions, which could help researchers to analyze 
      genetic data in a fast and scalable way. This article presents execution of the 
      BLAST algorithm on high performance computing (HPC) clusters and supercomputers 
      in a massively parallel manner using thousands of processors. The Parallel 
      Computing in Java (PCJ) library has been used to implement the optimal splitting 
      up of the input queries, the work distribution, and search management. It is used 
      with the nonmodified NCBI-BLAST package, which is an additional advantage for the 
      users. The result application-PCJ-BLAST-is responsible for reading sequence for 
      comparison, splitting it up and starting multiple NCBI-BLAST executables. Since 
      I/O performance could limit sequence analysis performance, the article contains 
      an investigation of this problem. The obtained results show that using Java and 
      PCJ library it is possible to perform sequence analysis using hundreds of nodes 
      in parallel. We have achieved excellent performance and efficiency and we have 
      significantly reduced the time required for sequence analysis. Our work also 
      proved that PCJ library could be used as an effective tool for fast development 
      of the scalable applications.
FAU - Nowicki, Marek
AU  - Nowicki M
AD  - 1 Faculty of Mathematics and Computer Science, Nicolaus Copernicus University in 
      Torun , Poland .
FAU - Bzhalava, Davit
AU  - Bzhalava D
AD  - 2 Department of Laboratory Medicine, Karolinska Institutet , Stockholm, Sweden .
FAU - BaLa, Piotr
AU  - BaLa P
AD  - 3 Interdisciplinary Center for Mathematical and Computational Modeling, 
      University of Warsaw , Warsaw, Poland .
LA  - eng
PT  - Journal Article
PT  - Research Support, Non-U.S. Gov't
DEP - 20180713
PL  - United States
TA  - J Comput Biol
JT  - Journal of computational biology : a journal of computational molecular cell 
      biology
JID - 9433358
SB  - IM
MH  - Computational Biology/*methods
MH  - *Computing Methodologies
MH  - Humans
MH  - Programming Languages
MH  - Sequence Alignment/*methods
MH  - *Software
OTO - NOTNLM
OT  - BLAST
OT  - Java
OT  - PCJ
OT  - next-generation sequencing
OT  - sequence alignment
EDAT- 2018/07/14 06:00
MHDA- 2019/10/24 06:00
CRDT- 2018/07/14 06:00
PHST- 2018/07/14 06:00 [pubmed]
PHST- 2019/10/24 06:00 [medline]
PHST- 2018/07/14 06:00 [entrez]
AID - 10.1089/cmb.2018.0079 [doi]
PST - ppublish
SO  - J Comput Biol. 2018 Aug;25(8):871-881. doi: 10.1089/cmb.2018.0079. Epub 2018 Jul 
      13.