ABS: Sequence alignment by scanning

Handle URI:
http://hdl.handle.net/10754/564415
Title:
ABS: Sequence alignment by scanning
Authors:
Bonny, Mohamed Talal; Salama, Khaled N. ( 0000-0001-7742-1282 )
Abstract:
Sequence alignment is an essential tool in almost any computational biology research. It processes large database sequences and considered to be high consumers of computation time. Heuristic algorithms are used to get approximate but fast results. We introduce fast alignment algorithm, called Alignment By Scanning (ABS), to provide an approximate alignment of two DNA sequences. We compare our algorithm with the well-known alignment algorithms, the FASTA (which is heuristic) and the 'Needleman-Wunsch' (which is optimal). The proposed algorithm achieves up to 76% enhancement in alignment score when it is compared with the FASTA Algorithm. The evaluations are conducted using different lengths of DNA sequences. © 2011 IEEE.
KAUST Department:
Electrical Engineering Program; Computer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division; Physical Sciences and Engineering (PSE) Division; Sensors Lab
Publisher:
Institute of Electrical and Electronics Engineers (IEEE)
Journal:
2011 Annual International Conference of the IEEE Engineering in Medicine and Biology Society
Conference/Event name:
33rd Annual International Conference of the IEEE Engineering in Medicine and Biology Society, EMBS 2011
Issue Date:
Aug-2011
DOI:
10.1109/IEMBS.2011.6090209
PubMed ID:
22254463
Type:
Conference Paper
ISSN:
1557170X
ISBN:
9781424441211
Appears in Collections:
Conference Papers; Physical Sciences and Engineering (PSE) Division; Electrical Engineering Program; Sensors Lab; Computer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division

Full metadata record

DC FieldValue Language
dc.contributor.authorBonny, Mohamed Talalen
dc.contributor.authorSalama, Khaled N.en
dc.date.accessioned2015-08-04T06:26:51Zen
dc.date.available2015-08-04T06:26:51Zen
dc.date.issued2011-08en
dc.identifier.isbn9781424441211en
dc.identifier.issn1557170Xen
dc.identifier.pmid22254463en
dc.identifier.doi10.1109/IEMBS.2011.6090209en
dc.identifier.urihttp://hdl.handle.net/10754/564415en
dc.description.abstractSequence alignment is an essential tool in almost any computational biology research. It processes large database sequences and considered to be high consumers of computation time. Heuristic algorithms are used to get approximate but fast results. We introduce fast alignment algorithm, called Alignment By Scanning (ABS), to provide an approximate alignment of two DNA sequences. We compare our algorithm with the well-known alignment algorithms, the FASTA (which is heuristic) and the 'Needleman-Wunsch' (which is optimal). The proposed algorithm achieves up to 76% enhancement in alignment score when it is compared with the FASTA Algorithm. The evaluations are conducted using different lengths of DNA sequences. © 2011 IEEE.en
dc.publisherInstitute of Electrical and Electronics Engineers (IEEE)en
dc.titleABS: Sequence alignment by scanningen
dc.typeConference Paperen
dc.contributor.departmentElectrical Engineering Programen
dc.contributor.departmentComputer, Electrical and Mathematical Sciences and Engineering (CEMSE) Divisionen
dc.contributor.departmentPhysical Sciences and Engineering (PSE) Divisionen
dc.contributor.departmentSensors Laben
dc.identifier.journal2011 Annual International Conference of the IEEE Engineering in Medicine and Biology Societyen
dc.conference.date30 August 2011 through 3 September 2011en
dc.conference.name33rd Annual International Conference of the IEEE Engineering in Medicine and Biology Society, EMBS 2011en
dc.conference.locationBoston, MAen
kaust.authorBonny, Mohamed Talalen
kaust.authorSalama, Khaled N.en

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