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Abstract: Techniques for detecting similarities between biological sequences such as proteins and DNA are used as a fundamental tool by biologists to investigate the relationships between such sequences. Most of the similarity techniques are based on notions of string edit sequence which involve sequence alignment using substitutions and deletions based on some cost measure. In this paper, we investigate algorithms which generalize the basic dynamic programming string edit distance algorithm to allow... (Update)
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BibTeX entry: (Update)
@article{ yap01parametric,
author = "Roland H. C. Yap",
title = "Parametric Sequence Alignment with Constraints",
journal = "Constraints",
volume = "6",
number = "2/3",
pages = "157-172",
year = "2001",
url = "citeseer.ist.psu.edu/467401.html" }
Citations (may not include all citations):431 A basic local alignment search tool (context) - Altschul, Gish et al. - 1990
270 The string-to-string correction problem (context) - Wagner, Fisher - 1974
247 A general method applicable to the search for similarities i.. (context) - Needleman, Wunsch - 1970
240 Identification of common molecular subsequences - Smith, Waterman - 1981
155 Improved tools for biological sequence comparison (context) - Pearson, Lipman - 1988
148 the theory and computation of evolutionary distances (context) - Sellers - 1970
147 and macromolecules: the theory and practice of sequence comp.. (context) - Sankoff, Kruskal et al. - 1983
81 Introduction to computational molecular biology (context) - Setubal, Meidanis - 1997
74 Amino acid substitution matrices from protein blocks (context) - Henikoff, Henikoff - 1992
60 A model of evolutionary change in proteins (context) - Dayhoff, Schwartz et al. - 1978
30 The rapid generation of mutation data matrices from protein .. (context) - Jones, Taylor et al. - 1992
28 Mathematical methods for DNA sequences (context) - Waterman - 1989
26 The CLP(R) Language and System (context) - Jaffar, Michaylov et al. - 1992
14 Empirical and Structural Models for Insertions and Deletions.. (context) - Benner, Cohen et al. - 1993
14 Parametric optimization of sequence alignment (context) - Gusfield, Balasubramanian et al. - 1992
10 Sequence alignment and penalty choice: review of concepts, c.. (context) - Vingron, Waterman - 1994
6 A Constraint Logic Programming Framework for Constructing DN.. (context) - Yap - 1993
5 Parametric sequence comparisons (context) - Waterman, Eggert et al. - 1992
3 A Restriction Mapping Engine using Constraint Logic Programm.. (context) - Dix, Yee - 1994
2 Sequence alignments in the neighborhood of the optimum with .. (context) - Waterman - 1983
2 Restriction Site Mapping in CLP(R (context) - Yap - 1991
1 Searching protein sequence databases -- Is optimal best (context) - Pearson - 1994
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