Fast global sequence alignment technique

Mohamed Talal Bonny; Khaled N. Salama

doi:10.1109/ACSSC.2011.6190171

Fast global sequence alignment technique

Mohamed Talal Bonny, Khaled N. Salama

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

1 Scopus citations

Abstract

Bioinformatics database is growing exponentially in size. Processing these large amount of data may take hours of time even if super computers are used. One of the most important processing tool in Bioinformatics is sequence alignment. 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 wellknown sequence alignment algorithms, the 'GAP' (which is heuristic) and the 'Needleman-Wunsch' (which is optimal). The proposed algorithm achieves up to 51% enhancement in alignment score when it is compared with the GAP Algorithm. The evaluations are conducted using different lengths of DNA sequences. © 2011 IEEE.

Original language	English (US)
Title of host publication	2011 Conference Record of the Forty Fifth Asilomar Conference on Signals, Systems and Computers (ASILOMAR)
Publisher	Institute of Electrical and Electronics Engineers (IEEE)
Pages	1046-1049
Number of pages	4
ISBN (Print)	9781467303231
DOIs	https://doi.org/10.1109/ACSSC.2011.6190171
State	Published - Nov 2011

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10.1109/ACSSC.2011.6190171

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@inproceedings{c190627fb65f4331a15c5e286139c81d,

title = "Fast global sequence alignment technique",

abstract = "Bioinformatics database is growing exponentially in size. Processing these large amount of data may take hours of time even if super computers are used. One of the most important processing tool in Bioinformatics is sequence alignment. 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 wellknown sequence alignment algorithms, the 'GAP' (which is heuristic) and the 'Needleman-Wunsch' (which is optimal). The proposed algorithm achieves up to 51% enhancement in alignment score when it is compared with the GAP Algorithm. The evaluations are conducted using different lengths of DNA sequences. {\textcopyright} 2011 IEEE.",

author = "Bonny, {Mohamed Talal} and Salama, {Khaled N.}",

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year = "2011",

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T1 - Fast global sequence alignment technique

AU - Bonny, Mohamed Talal

AU - Salama, Khaled N.

N1 - KAUST Repository Item: Exported on 2020-10-01

PY - 2011/11

Y1 - 2011/11

N2 - Bioinformatics database is growing exponentially in size. Processing these large amount of data may take hours of time even if super computers are used. One of the most important processing tool in Bioinformatics is sequence alignment. 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 wellknown sequence alignment algorithms, the 'GAP' (which is heuristic) and the 'Needleman-Wunsch' (which is optimal). The proposed algorithm achieves up to 51% enhancement in alignment score when it is compared with the GAP Algorithm. The evaluations are conducted using different lengths of DNA sequences. © 2011 IEEE.

AB - Bioinformatics database is growing exponentially in size. Processing these large amount of data may take hours of time even if super computers are used. One of the most important processing tool in Bioinformatics is sequence alignment. 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 wellknown sequence alignment algorithms, the 'GAP' (which is heuristic) and the 'Needleman-Wunsch' (which is optimal). The proposed algorithm achieves up to 51% enhancement in alignment score when it is compared with the GAP Algorithm. The evaluations are conducted using different lengths of DNA sequences. © 2011 IEEE.

UR - http://hdl.handle.net/10754/564456

UR - http://ieeexplore.ieee.org/document/6190171/

UR - http://www.scopus.com/inward/record.url?scp=84861325025&partnerID=8YFLogxK

U2 - 10.1109/ACSSC.2011.6190171

DO - 10.1109/ACSSC.2011.6190171

M3 - Conference contribution

SN - 9781467303231

SP - 1046

EP - 1049

BT - 2011 Conference Record of the Forty Fifth Asilomar Conference on Signals, Systems and Computers (ASILOMAR)

PB - Institute of Electrical and Electronics Engineers (IEEE)

ER -

Fast global sequence alignment technique

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