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Bulletin of Mathematical Biology
Article . 1993 . Peer-reviewed
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Article . 1993 . Peer-reviewed
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Constrained sequence alignment

descriptionPublicationkeyboard_double_arrow_right Article 01 May 1993 English Publisher:Springer Science and Business Media LLCJournal:Bulletin of Mathematical Biology, volume 55, pages 503-524 (issn: 0092-8240, Copyright policy )
Authors: Chao, Kun-Mao; Hardison, Ross C.; Miller, Webb;

doi: 10.1016/s0092-8240(05)80237-x , 10.1007/bf02460648

pmid: 8298508

Constrained sequence alignment

Abstract

This paper presents a dynamic programming algorithm for aligning two sequences when the alignment is constrained to lie between two arbitrary boundary lines in the dynamic programming matrix. For affine gap penalties, the algorithm requires only O(F) computations time and O(M+N) space, when F is the area of the feasible region and M and N are the sequence lengths. The result extends to concave gap penalities, with somewhat increased time and space bounds.

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Keywords

concave gap penalties, Nicotiana, Chloroplasts, Genome, Biochemistry, molecular biology, DNA, Plants, constrained sequence alignment, Plants, Toxic, Applications of mathematical programming, protein sequences, Computational methods for problems pertaining to biology, Semi-infinite programming, Sequence Alignment, affine gap penalties, Algorithms

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    		 17
    popularity
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selected citations
These citations are derived from selected sources.
This is an alternative to the "Influence" indicator, which also reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
BIP!Citations provided by BIP!
popularity
This indicator reflects the "current" impact/attention (the "hype") of an article in the research community at large, based on the underlying citation network.
BIP!Popularity provided by BIP!
influence
This indicator reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
BIP!Influence provided by BIP!
impulse
This indicator reflects the initial momentum of an article directly after its publication, based on the underlying citation network.
BIP!Impulse provided by BIP!
17
Average
Top 10%
Top 10%
bronze