NDLI: Handling Updates of a Pairwise Sequence Alignment

Content Provider	IEEE Xplore Digital Library
Author	Changjin Hong Tewfik, A.H.
Copyright Year	2006
Description	Author affiliation: Dept. of Electr. & Comput. Eng., Minnesota Univ. (Changjin Hong; Tewfik, A.H.)
Abstract	Sequence alignment or decoding in molecular biology is mostly done via computationally expensive dynamic programming (DP) based approaches. Unfortunately, as sequencing errors are discovered frequently, researchers must repeat all previous similarity analysis for the erroneous sequence. This can take hours or days. In this work, we derive relative tolerance bounds on node distances from a root node that guarantee that partial shortest path distances remain optimal. We then propose an algorithm that uses these bounds to skip all unperturbed parts of a sequence when recomputing an alignment. We also discuss techniques to reduce the memory requirements of the algorithm by focusing on the highly conserved segments of the sequence. Experimental results establish that our proposed alignment procedure can update alignment decisions of modified sequence with 4.6% to 18% of the number of computations required by the normal Needleman-Wunsch algorithm, depending on sequence length. Higher computational savings are achieved with longer sequences
Sponsorship	The Inst. of Electr. and Electron. Eng., Inc. Circuits and Syst. Soc. (IEEE CASS)
File Size	136240
File Format	PDF
ISBN	142440469X
ISSN	15206149
DOI	10.1109/ICASSP.2006.1660540
Language	English
Publisher	Institute of Electrical and Electronics Engineers, Inc. (IEEE)
Publisher Date	2006-05-14
Publisher Place	France
Access Restriction	Subscribed
Rights Holder	Institute of Electrical and Electronics Engineers, Inc. (IEEE)
Subject Keyword	Sequences Tree graphs Biology computing Decoding Biological information theory Dynamic programming Computer errors Databases Polymers Collaboration
Content Type	Text
Resource Type	Article

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