ABS: Sequence alignment by scanning

Mohamed Talal Bonny, Khaled N. Salama

Research output: Chapter in Book/Report/Conference proceedingConference contribution

3 Scopus citations

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.
Original languageEnglish (US)
Title of host publication2011 Annual International Conference of the IEEE Engineering in Medicine and Biology Society
PublisherInstitute of Electrical and Electronics Engineers (IEEE)
Pages928-931
Number of pages4
ISBN (Print)9781424441211
DOIs
StatePublished - Aug 2011

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