Results 1  10
of
163
Optimal spaced seeds for faster approximate string matching
"... Filtering is a standard technique for fast approximate string matching in practice. In fi#12;ltering, a quick #12;first step is used to rule out almost all positions of a text as possible starting positions for a pattern. Typically this step consists of fi#12;nding the exact matches of small parts o ..."
Abstract

Cited by 8 (0 self)
 Add to MetaCart
Filtering is a standard technique for fast approximate string matching in practice. In fi#12;ltering, a quick #12;first step is used to rule out almost all positions of a text as possible starting positions for a pattern. Typically this step consists of fi#12;nding the exact matches of small parts
Optimal spaced seeds for faster approximate string matching
"... Filtering is a standard technique for fast approximate string matching in practice. In filtering, a quick first step is used to rule out almost all positions of a text as possible starting positions for a pattern. Typically this step consists of finding the exact matches of small parts of the patter ..."
Abstract
 Add to MetaCart
Filtering is a standard technique for fast approximate string matching in practice. In filtering, a quick first step is used to rule out almost all positions of a text as possible starting positions for a pattern. Typically this step consists of finding the exact matches of small parts
Faster String Matching With Super{alphabets
 Information Processing Letters
, 2002
"... Given a text T [1 : : : n] and a pattern P [1 : : : m] over some alphabet of size , nding the exact occurrences of P in T requires at least (n log m=m) character comparisons on average, as shown in [19]. Consequently, it is believed that this lower bound implies also an (n log m=m) lower ..."
Abstract
 Add to MetaCart
sux automaton. The space usage of the algorithm is O(m). The technique can be applied to many other string matching algorithms, including dictionary matching, which is also solved in expected time O(n=m), and approximate matching allowing k edit operations (mismatches, insertions or deletions
Faster Algorithms for String Matching Problems: Matching the Convolution Bound
 In Proceedings of the 39th Symposium on Foundations of Computer Science
, 1998
"... In this paper we give a randomized O(n log n)time algorithm for the string matching with don't cares problem. This improves the FischerPaterson bound [10] from 1974 and answers the open problem posed (among others) by Weiner [30] and Galil [11]. Using the same technique, we give an O(n log ..."
Abstract

Cited by 37 (3 self)
 Add to MetaCart
In this paper we give a randomized O(n log n)time algorithm for the string matching with don't cares problem. This improves the FischerPaterson bound [10] from 1974 and answers the open problem posed (among others) by Weiner [30] and Galil [11]. Using the same technique, we give an O
Averageoptimal single and multiple approximate string matching
 ACM Journal of Experimental Algorithmics (JEA
"... Abstract. We present a new algorithm for multiple approximate string matching. It is based on reading backwards enough ℓgrams from text windows so as to prove that no occurrence can contain the part of the window read, and then shifting the window. Three variants of the algorithm are presented, whi ..."
Abstract

Cited by 20 (9 self)
 Add to MetaCart
], the new algorithms are much faster and are optimal up to difference ratios of 1/2, contrary to the maximum of 1/3 that could be reached in previous work. This is also a contribution to the area of singlepattern approximate string matching, as the only averageoptimal algorithm [Chang and Marr, CPM 1994
Approximate string matching using compressed suffix arrays
 In Proceedings of Symposium on Combinatorial Pattern Matching
, 2004
"... Abstract. Let T be a text of length n and P be a pattern of length m, bothstrings over a fixed finite alphabet A. The kdifference (kmismatch, respectively)problem is to find all occurrences of P in T that have edit distance (Hammingdistance, respectively) at most k from P. In this paper we investi ..."
Abstract

Cited by 28 (2 self)
 Add to MetaCart
text of length n and P be a pattern of length m, both strings over a fixedfinite alphabet A. The string matching problem is to find all occurrences of P in T whichsatisfy some criteria. Depending on the criteria, we have three different problems. (1)
Bitparallel Witnesses and their Applications to Approximate String Matching
 Algorithmica
, 2005
"... We present a new bitparallel technique for approximate string matching. We build on two previous techniques. The first one, BPM [Myers, J. of the ACM, 1999], searches for a pattern of length m in a text of length n permitting k differences in O(⌈m/w⌉n) time, where w is the width ..."
Abstract

Cited by 21 (2 self)
 Add to MetaCart
We present a new bitparallel technique for approximate string matching. We build on two previous techniques. The first one, BPM [Myers, J. of the ACM, 1999], searches for a pattern of length m in a text of length n permitting k differences in O(⌈m/w⌉n) time, where w
Improved Single and Multiple Approximate String Matching
 ACM Journal of Experimental Algorithmics (JEA
"... We present a new algorithm for multiple approximate string matching. It is based on reading backwards enough lgrams from text windows so as to prove that no occurrence can contain the part of the window read, and then shifting the window. Three variants of the algorithm are presented, which give di ..."
Abstract

Cited by 1 (1 self)
 Add to MetaCart
are much faster and are optimal up to difference ratios of 1/2, contrary to the maximum of 1/3 that could be reached in previous work. This is also a contribution to the area of singlepattern approximate string matching, as the only averageoptimal algorithm [Chang and Marr, CPM 1994] also reached a
Compression of Strings with Approximate Repeats
 Intelligent Systems in Molecular Biology, ISMB ’98
, 1998
"... We describe a model for strings of characters that is loosely based on the Lempel Ziv model with the addition that a repeated substring can be an approximate match to the original substring; this is close to the situation of DNA, for example. Typically there are many explanations for a given string ..."
Abstract

Cited by 10 (3 self)
 Add to MetaCart
We describe a model for strings of characters that is loosely based on the Lempel Ziv model with the addition that a repeated substring can be an approximate match to the original substring; this is close to the situation of DNA, for example. Typically there are many explanations for a given string
Hardness of optimal spaced seed design
 PARK (EDS.), PROCEEDINGS OF THE 16TH ANNUAL SYMPOSIUM ON COMBINATORIAL PATTERN MATCHING (CPM’05)
, 2005
"... Speeding up approximate pattern matching is a line of research in stringology since the 80’s. Practically fast approaches belong to the class of filtration algorithms, in which text regions dissimilar to the pattern are first excluded, and the remaining regions are then compared to the pattern by dy ..."
Abstract

Cited by 22 (1 self)
 Add to MetaCart
Speeding up approximate pattern matching is a line of research in stringology since the 80’s. Practically fast approaches belong to the class of filtration algorithms, in which text regions dissimilar to the pattern are first excluded, and the remaining regions are then compared to the pattern
Results 1  10
of
163