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Massively parallel sequence alignment with BLAST Through Work Distribution implemented Using PCJ Library

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cris.lastimport.scopus2024-02-12T20:56:13Z
dc.abstract.enThis 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.
dc.affiliationUniwersytet Warszawski
dc.conference.countryFinlandia
dc.conference.datefinish2017-08-23
dc.conference.datestart2017-08-21
dc.conference.placeHelsinki
dc.conference.seriesInternational Conference on Algorithms and Architectures for Parallel Processing
dc.conference.seriesInternational Conference on Algorithms and Architectures for Parallel Processing
dc.conference.seriesshortcutICA3PP
dc.conference.shortcutICA3PP 2017
dc.conference.weblinkhttps://link.springer.com/book/10.1007/978-3-319-65482-9
dc.contributor.authorNowicki, Marek
dc.contributor.authorBała, Piotr
dc.contributor.authorBzhalava, Davit
dc.date.accessioned2024-01-25T05:33:40Z
dc.date.available2024-01-25T05:33:40Z
dc.date.issued2017
dc.description.financeNie dotyczy
dc.identifier.doi10.1007/978-3-319-65482-9_36
dc.identifier.urihttps://repozytorium.uw.edu.pl//handle/item/111884
dc.identifier.weblinkhttps://link.springer.com/chapter/10.1007%2F978-3-319-65482-9_36
dc.languageeng
dc.pbn.affiliationcomputer and information sciences
dc.relation.pages503-512
dc.rightsClosedAccess
dc.sciencecloudnosend
dc.subject.enSequence alignment
dc.subject.enNGS
dc.subject.enNext Generation Sequencing
dc.subject.enParallel programming
dc.subject.enJava
dc.subject.enBLAST
dc.subject.enNCBI-BLAST
dc.subject.enPCJ
dc.titleMassively parallel sequence alignment with BLAST Through Work Distribution implemented Using PCJ Library
dc.typeJournalArticle
dspace.entity.typePublication