Publication:
Parallelizing Optimal Multiple Sequence Alignment by Dynamic Programming
Parallelizing Optimal Multiple Sequence Alignment by Dynamic Programming
dc.contributor.author | Helal, Manal | en_US |
dc.contributor.author | El-Gindy, Hossam | en_US |
dc.contributor.author | Gaeta, Bruno | en_US |
dc.contributor.author | Mullin, Lenore | en_US |
dc.date.accessioned | 2021-11-25T12:46:24Z | |
dc.date.available | 2021-11-25T12:46:24Z | |
dc.date.issued | 2008 | en_US |
dc.description.abstract | Optimal multiple sequence alignment by dynamic programming, like many highly dimensional scientific computing problems, has failed to benefit from the improvements in computing performance brought about by multi-processor systems, due to the lack of suitable scheme to manage partitioning and dependencies. A scheme for parallel implementation of the dynamic programming multiple sequence alignment is presented, based on a peer to peer design and a multidimensional array indexing method. This design results in up to 5-fold improvement compared to a previously described master/slave design, and scales favourably with the number of processors used. This study demonstrates an approach for parallelising multi-dimensional dynamic programming and similar algorithms utilizing multi-processor architectures. | en_US |
dc.identifier.uri | http://hdl.handle.net/1959.4/37298 | |
dc.language | English | |
dc.language.iso | EN | en_US |
dc.rights | CC BY-NC-ND 3.0 | en_US |
dc.rights.uri | https://creativecommons.org/licenses/by-nc-nd/3.0/au/ | en_US |
dc.source | Legacy MARC | en_US |
dc.subject.other | Multiple Sequence Alignment | en_US |
dc.subject.other | Parallel Algorithms | en_US |
dc.subject.other | Dynamic Programming | en_US |
dc.subject.other | Computational Biology | en_US |
dc.subject.other | Mathematical Computing | en_US |
dc.subject.other | High Performance Computing | en_US |
dc.subject.other | High Dimensional Problems | en_US |
dc.subject.other | 280499 Computation Theory and Mathematics not elsewhere classified | en_US |
dc.title | Parallelizing Optimal Multiple Sequence Alignment by Dynamic Programming | en_US |
dc.type | Conference Paper | en |
dcterms.accessRights | open access | |
dspace.entity.type | Publication | en_US |
unsw.accessRights.uri | https://purl.org/coar/access_right/c_abf2 | |
unsw.description.publisherStatement | © 2008 IEEE. Personal use of this material is permitted. However, permission to reprint/republish this material for advertising or promotional purposes or for creating new collective works for resale or redistribution to servers or lists, or to reuse any copyrighted component of this work in other works must be obtained from the IEEE. | en_US |
unsw.identifier.doiPublisher | http://dx.doi.org/10.1109/ISPA.2008.93 | en_US |
unsw.relation.faculty | Engineering | |
unsw.relation.ispartofconferenceLocation | Sydney, Australia | en_US |
unsw.relation.ispartofconferenceName | International Symposium on Advances in Parallel and Distributed Computing Techniques (APDCT-08) | en_US |
unsw.relation.ispartofconferenceProceedingsTitle | International Symposium on Parallel and Distributed Processing with Applications (ISPA '08) | en_US |
unsw.relation.ispartofconferenceYear | 2008 | en_US |
unsw.relation.ispartofpagefrompageto | 669-674 | en_US |
unsw.relation.originalPublicationAffiliation | Helal, Manal , Computer Science & Engineering, Faculty of Engineering, UNSW | en_US |
unsw.relation.originalPublicationAffiliation | El-Gindy, Hossam, Computer Science & Engineering, Faculty of Engineering, UNSW | en_US |
unsw.relation.originalPublicationAffiliation | Gaeta, Bruno, Computer Science & Engineering, Faculty of Engineering, UNSW | en_US |
unsw.relation.originalPublicationAffiliation | Mullin, Lenore, National Science Foundation - USA | en_US |
unsw.relation.school | School of Computer Science and Engineering | * |
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