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Abstract: Introduction Aligning two short, similiar protein sequences by eye is an easy task. Teaching a machine the same skill turns out to be astonishingly difficult. Starting with the famous paper by Needleman and Wunsch [1] people have used dynamic programming algorithms to maximize the score associated with an alignment. While this algorithm is sometimes perceived as complicated the definition of an optimal sequence alignment is not. It is, in fact, simple. For proteins, pairs of residues are... (Update)
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BibTeX entry: (Update)
M. Vingron, "Near--Optimal Sequence Alignment," Curr. Op. Struct. Biology, Vol. 6, No. 3, pp. 346--352, June 1996. http://citeseer.ist.psu.edu/vingron96nearoptimal.html More
@article{ vingron96nearoptimal,
author = "Martin Vingron",
title = "{Near-optimal sequence alignment}",
journal = "Current Opinion in Structural Biology",
volume = "6",
number = "3",
month = "June",
pages = "346--352",
year = "1996",
url = "citeseer.ist.psu.edu/vingron96nearoptimal.html" }
Citations (may not include all citations):38 Rivest: Introduction to Algorithms (context) - Cormen, Leiserson - 1990
15 linear-space local similarity algorithm (context) - Huang, Miller et al. - 1991
14 and multiple biological sequence alignment (context) - Altschul, Lipman et al. - 1989
5 Wunsch: A general method applicable to the search for simila.. (context) - Needleman - 1970
5 Waterman: Identification of common molecular subsequences (context) - Smith - 1981
2 Argos: Determination of reliable regions in protein sequence.. (context) - Vingron - 1990
2 Eggert: A new algorithm for best subsequence alignments with.. (context) - Waterman - 1987
2 Lipman: Basic local alignment search tool (context) - Altschul, Gish et al. - 1990
1 Miller: Recent developments in linear-space alignment method.. (context) - Chao, Hardison - 1994
1 in molecular biol (context) - Zuker, alignment - 1991
1 Lipman: The multiple sequence alignment problem in biology (context) - Carrillo - 1988
1 1:349--366 (context) - Naor, Brutlag et al. - 1994
1 Kececioglu: A tool for multiple sequence alignment (context) - Lipman, Altschul - 1989
1 Waterman: Sequence alignment and penalty choice: Review of c.. (context) - Vingron - 1994
1 Schaeffer: Improving the practical space and time efficiency.. (context) - Gupta, Kececioglu - 1995
[Article contains additional citations not shown here]
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Quantifying the Local Reliability of a Sequence Alignment - Mevissen, Vingron (1996) (Correct)
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