Weighted shortest common supersequence

Amihood Amir; Zvi Gotthilf; B. Riva Shalom

doi:10.1007/978-3-642-24583-1_6

Weighted shortest common supersequence

Amihood Amir, Zvi Gotthilf, B. Riva Shalom

Department of Computer Science

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

3 Scopus citations

Abstract

The Shortest Common Supersequence (SCS) is the problem of seeking a shortest possible sequence that contains each of the input sequences as a subsequence. In this paper we consider applying the problem to 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 SCS on PWM. For the first, we give a polynomial time algorithm, having two input sequences. For the second, we prove NP-hardness.

Original language	English
Title of host publication	String Processing and Information Retrieval - 18th International Symposium, SPIRE 2011, Proceedings
Pages	44-54
Number of pages	11
DOIs	https://doi.org/10.1007/978-3-642-24583-1_6
State	Published - 2011
Event	18th International Symposium on String Processing and Information Retrieval, SPIRE 2011 - Pisa, Italy Duration: 17 Oct 2011 → 21 Oct 2011

Publication series

Name	Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Volume	7024 LNCS
ISSN (Print)	0302-9743
ISSN (Electronic)	1611-3349

Conference

Conference	18th International Symposium on String Processing and Information Retrieval, SPIRE 2011
Country/Territory	Italy
City	Pisa
Period	17/10/11 → 21/10/11

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10.1007/978-3-642-24583-1_6

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Amir, A., Gotthilf, Z., & Shalom, B. R. (2011). Weighted shortest common supersequence. In String Processing and Information Retrieval - 18th International Symposium, SPIRE 2011, Proceedings (pp. 44-54). (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vol. 7024 LNCS). https://doi.org/10.1007/978-3-642-24583-1_6

@inproceedings{f204ddeeb2604edba8b0318ef3aed87e,

title = "Weighted shortest common supersequence",

abstract = "The Shortest Common Supersequence (SCS) is the problem of seeking a shortest possible sequence that contains each of the input sequences as a subsequence. In this paper we consider applying the problem to 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 SCS on PWM. For the first, we give a polynomial time algorithm, having two input sequences. For the second, we prove NP-hardness.",

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

year = "2011",

doi = "10.1007/978-3-642-24583-1_6",

language = "אנגלית",

isbn = "9783642245824",

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

pages = "44--54",

booktitle = "String Processing and Information Retrieval - 18th International Symposium, SPIRE 2011, Proceedings",

note = "18th International Symposium on String Processing and Information Retrieval, SPIRE 2011 ; Conference date: 17-10-2011 Through 21-10-2011",

}

Amir, A, Gotthilf, Z & Shalom, BR 2011, Weighted shortest common supersequence. in String Processing and Information Retrieval - 18th International Symposium, SPIRE 2011, Proceedings. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), vol. 7024 LNCS, pp. 44-54, 18th International Symposium on String Processing and Information Retrieval, SPIRE 2011, Pisa, Italy, 17/10/11. https://doi.org/10.1007/978-3-642-24583-1_6

Weighted shortest common supersequence. / Amir, Amihood; Gotthilf, Zvi; Shalom, B. Riva.
String Processing and Information Retrieval - 18th International Symposium, SPIRE 2011, Proceedings. 2011. p. 44-54 (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vol. 7024 LNCS).

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

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Weighted shortest common supersequence

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