Weighted LCS

Amihood Amir; Zvi Gotthilf; B. Riva Shalom

doi:10.1007/978-3-642-10217-2_7

Weighted LCS

Amihood Amir, Zvi Gotthilf, B. Riva Shalom

Department of Computer Science

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › peer-review

2 Scopus citations

Abstract

The Longest Common Subsequence (LCS) of two strings A and B is a well studied problem having awide range of applications. When each symbol of the input strings is assigned a positive weight the problem becomes the Heaviest Common Subsequence (HCS) problem. In this paper we consider a different version of weighted LCS on Position Weight Matrices (PWM). The Position Weight Matrix was introduced as a tool to handle a set of sequences that are not identical, yet, have many local similarities. Such a weighted sequence is a 'statistical image' of this set where we are given the probability of every symbol's occurrence at every text location. We consider two possible definitions of LCS on PWM. For the first, we solve the weighted LCS problem of z sequences in time O(zn^z+1). For the second, we prove NP-hardness and provide an approximation algorithm.

Original language	English
Title of host publication	Combinatorial Algorithms - 20th International Workshop, IWOCA 2009, Revised Selected Papers
Pages	36-47
Number of pages	12
DOIs	https://doi.org/10.1007/978-3-642-10217-2_7
State	Published - 2009
Event	20th International Workshop on Combinatorial Algorithms, IWOCA 2009 - Hradec nad Moravici, Czech Republic Duration: 28 Jun 2009 → 2 Jul 2009

Publication series

Name	Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Volume	5874 LNCS
ISSN (Print)	0302-9743
ISSN (Electronic)	1611-3349

Conference

Conference	20th International Workshop on Combinatorial Algorithms, IWOCA 2009
Country/Territory	Czech Republic
City	Hradec nad Moravici
Period	28/06/09 → 2/07/09

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10.1007/978-3-642-10217-2_7

Cite this

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title = "Weighted LCS",

abstract = "The Longest Common Subsequence (LCS) of two strings A and B is a well studied problem having awide range of applications. When each symbol of the input strings is assigned a positive weight the problem becomes the Heaviest Common Subsequence (HCS) problem. In this paper we consider a different version of weighted LCS on Position Weight Matrices (PWM). The Position Weight Matrix was introduced as a tool to handle a set of sequences that are not identical, yet, have many local similarities. Such a weighted sequence is a 'statistical image' of this set where we are given the probability of every symbol's occurrence at every text location. We consider two possible definitions of LCS on PWM. For the first, we solve the weighted LCS problem of z sequences in time O(znz+1). For the second, we prove NP-hardness and provide an approximation algorithm.",

author = "Amihood Amir and Zvi Gotthilf and Shalom, {B. Riva}",

year = "2009",

doi = "10.1007/978-3-642-10217-2_7",

language = "אנגלית",

isbn = "3642102166",

series = "Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)",

pages = "36--47",

booktitle = "Combinatorial Algorithms - 20th International Workshop, IWOCA 2009, Revised Selected Papers",

note = "20th International Workshop on Combinatorial Algorithms, IWOCA 2009 ; Conference date: 28-06-2009 Through 02-07-2009",

}

Amir, A, Gotthilf, Z & Shalom, BR 2009, Weighted LCS. in Combinatorial Algorithms - 20th International Workshop, IWOCA 2009, Revised Selected Papers. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), vol. 5874 LNCS, pp. 36-47, 20th International Workshop on Combinatorial Algorithms, IWOCA 2009, Hradec nad Moravici, Czech Republic, 28/06/09. https://doi.org/10.1007/978-3-642-10217-2_7

Weighted LCS. / Amir, Amihood; Gotthilf, Zvi; Shalom, B. Riva.
Combinatorial Algorithms - 20th International Workshop, IWOCA 2009, Revised Selected Papers. 2009. p. 36-47 (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vol. 5874 LNCS).

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › peer-review

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Weighted LCS

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