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Efficient string matching with k differences. by Gad M. Landau

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Published by Courant Institute of Mathematical Sciences, New York University in New York .
Written in English


Book details:

Edition Notes

StatementBy Gad M. Landau, Uzi Vishkin.
ContributionsVishkin, U.
The Physical Object
Pagination16 p.
Number of Pages16
ID Numbers
Open LibraryOL17979344M

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NYU COMPSCI TR Landau, Gad M Efficient string matching with k differences. c,l Landau AUTHOR Electrodynamics of TITLE continuous media. DATE DUE BORROWER'S NAME Kc\)) v\ Sr /> YY^dA This book may be kept FOURTEEN DAYS A fine . An efficient string matching algorithm with k differences for nucleotide and amino acid sequences Gad , Uzi Vishkin1 and Ruth Nussinov2* Department of Computer Science, School of Mathematical Sciences, Tel Aviv University, Tel Aviv, Israel, 'Department of Computer Science, Courant Institute of Mathematical Sciences, New York University. EFFICIENT STRING MATCHING WITH k MISMATCHES Gad M. LANDAU Department of Computer Science, School of Mathematical Sciences, Tel Aviv University, Tel Aviv, Israel Uzi VISHKIN * Department of Computer Science, Courant Institute of Mathematical Sciences, New York University, New York, NY , U.S.A.   Given two strings P and T, m=|P|, n=|T|, mstring matching with k mismatches (SMk) is the one of finding all the occurrences of P in T with at most kk=0, and O(m log m+nk) for k> follow a new approach to SMk based on the determination of the permutations of P in T, and propose two.

  The k-differences problem should be distinguished from the easier problem of string matching with k mismatches (the k-mismatches problem for short). The k-mismatches problem is to find all occurrences of the pattern in the text with at most k differences of type (a), where differences of type (b) or (c) are not allowed.   Theoretical Computer Science 43 () North-Holland EFFICIENT STRING MATCHING WITH k MISMATCHES Gad M. LANDAU Department of Computer Science, School of Mathematical Sciences, Tel Aviv University, Tel Aviv, Israel Uzi VISHKIN * Department of Computer Science, Courant Institute of Mathematical Sciences, New York University, New York, NY , .   J. theor. Biol. () , An Efficient String Matching Algorithm with K Substitutions for Nucleotide and Amino Acid Sequences GAD M. LANDAU AND UzI VISHKIN1 Department of Computer Science, School of Mathematical Sciences, Tel Aviv University, Tel Aviv , Israel and ~Department of Computer Science, Courant Institute of Mathematical Sciences, New York . Approximate String Matching problem: Find all text locations where distance from pattern is sufficiently small. distance metric: HAMMING DISTANCE Let S = s 1 s 2 s m R = r 1 r 2 r m Ham(S,R) = The number of locations j where s j r j Example: S = ABCABC R = ABBAAC Ham(S,R) = 2 z.

  An efficient string matching algorithm with k differences for nucleotide and amino acid sequences. deletions and insertions. Algorithms to date run in O(mn) time. Let us define an integer, k, which is the maximal number of differences allowed. We present a simple algorithm showing that sequences can be optimally aligned in O(k2n) time. For. Efficient string matching in the presence of errors Abstract: Consider the string matching problem where differences between characters of the pattern and characters of the text are allowed. Each difference is due to either a mismatch between a character of the text and a character of the pattern or a superfluous character in the text or a. The occurrences of a constant pattern in a given text string can be found in linear time using the famous algorithm of Knuth, Morris, and Pratt [KMP]. Aho and Corasick [AC] independently solved the problem for patterns consisting of a set of strings, where the occurrence of one member is considered a match. KEY WORDS String matching Edit distance k differences problem INTRODUCTION We considerthe k differencesproblem, a version of the approximate string matching problem. Given two strings, text T = t1 t n and pattern P p1 p m and integer k, the task is to find the end points of all approximate occurrences of P in T. An approximate.