The String-to-String Correction Problem
TL;DR: An algorithm is presented which solves the string-to-string correction problem in time proportional to the product of the lengths of the two strings.
Abstract: The string-to-string correction problem is to determine the distance between two strings as measured by the minimum cost sequence of “edit operations” needed to change the one string into the other. The edit operations investigated allow changing one symbol of a string into another single symbol, deleting one symbol from a string, or inserting a single symbol into a string. An algorithm is presented which solves this problem in time proportional to the product of the lengths of the two strings. Possible applications are to the problems of automatic spelling correction and determining the longest subsequence of characters common to two strings.
Citations
More filters
TL;DR: The CHARMM (Chemistry at Harvard Macromolecular Mechanics) as discussed by the authors is a computer program that uses empirical energy functions to model macromolescular systems, and it can read or model build structures, energy minimize them by first- or second-derivative techniques, perform a normal mode or molecular dynamics simulation, and analyze the structural, equilibrium, and dynamic properties determined in these calculations.
Abstract: CHARMM (Chemistry at HARvard Macromolecular Mechanics) is a highly flexible computer program which uses empirical energy functions to model macromolecular systems. The program can read or model build structures, energy minimize them by first- or second-derivative techniques, perform a normal mode or molecular dynamics simulation, and analyze the structural, equilibrium, and dynamic properties determined in these calculations. The operations that CHARMM can perform are described, and some implementation details are given. A set of parameters for the empirical energy function and a sample run are included.
14,725 citations
TL;DR: This work surveys the current techniques to cope with the problem of string matching that allows errors, and focuses on online searching and mostly on edit distance, explaining the problem and its relevance, its statistical behavior, its history and current developments, and the central ideas of the algorithms.
Abstract: We survey the current techniques to cope with the problem of string matching that allows errors. This is becoming a more and more relevant issue for many fast growing areas such as information retrieval and computational biology. We focus on online searching and mostly on edit distance, explaining the problem and its relevance, its statistical behavior, its history and current developments, and the central ideas of the algorithms and their complexities. We present a number of experiments to compare the performance of the different algorithms and show which are the best choices. We conclude with some directions for future work and open problems.
2,723 citations
TL;DR: The goal of this paper is to give Hirschberg's idea the visibility it deserves by developing a linear-space version of Gotoh's algorithm, which accommodates affine gap penalties.
Abstract: Space, not time, is often the limiting factor when computing optimal sequence alignments, and a number of recent papers in the biology literature have proposed space-saving strategies. However, a 1975 computer science paper by Hirschberg presented a method that is superior to the new proposals, both in theory and in practice. The goal of this paper is to give Hirschberg's idea the visibility it deserves by developing a linear-space version ofGotoh's algorithm, which accommodates affine gap penalties. A portable C-software package implementing this algorithm is available on the BIONET free of charge.
1,513 citations
TL;DR: The wide scope of repeat analysis is circumscribes using applications in five different areas of sequence analysis: checking fragment assemblies, searching for low copy repeats, finding unique sequences, comparing gene structures and mapping of cDNA/EST sequences.
Abstract: The repetitive structure of genomic DNA holds many secrets to be discovered. A systematic study of repetitive DNA on a genomic or inter-genomic scale requires extensive algorithmic support. The REPuter program described herein was designed to serve as a fundamental tool in such studies. Efficient and complete detection of various types of repeats is provided together with an evaluation of significance and interactive visualization. This article circumscribes the wide scope of repeat analysis using applications in five different areas of sequence analysis: checking fragment assemblies, searching for low copy repeats, finding unique sequences, comparing gene structures and mapping of cDNA/EST sequences.
1,460 citations
Cites background from "The String-to-String Correction Pro..."
...One could of course use a standard dynamic programming (DP) algorithm [for example see Wagner and Fischer (18)] to extend seeds in O(n2) time....
[...]
TL;DR: Research aimed at correcting words in text has focused on three progressively more difficult problems: nonword error detection; (2) isolated-word error correction; and (3) context-dependent work correction, which surveys documented findings on spelling error patterns.
Abstract: Research aimed at correcting words in text has focused on three progressively more difficult problems:(1) nonword error detection; (2) isolated-word error correction; and (3) context-dependent work correction. In response to the first problem, efficient pattern-matching and n-gram analysis techniques have been developed for detecting strings that do not appear in a given word list. In response to the second problem, a variety of general and application-specific spelling correction techniques have been developed. Some of them were based on detailed studies of spelling error patterns. In response to the third problem, a few experiments using natural-language-processing tools or statistical-language models have been carried out. This article surveys documented findings on spelling error patterns, provides descriptions of various nonword detection and isolated-word error correction techniques, reviews the state of the art of context-dependent word correction techniques, and discusses research issues related to all three areas of automatic error correction in text.
1,417 citations
References
More filters
TL;DR: By using systems which perform spelling correction, the number of debugging runs per program has been decreased, saving both programmer and machine time.
Abstract: Several specialized techniques are shown for efficiently incorporating spelling correction algorithms into compilers and operating systems. These include the use of syntax and semantics information, the organization of restricted keyword and symbol tables, and the consideration of a limited class of spelling errors. Sample 360 coding for performing spelling correction is presented. By using systems which perform spelling correction, the number of debugging runs per program has been decreased, saving both programmer and machine time.
118 citations