Normalized similarity of RNA sequences

Rolf Backofen; Danny Hermelin; Gad M. Landau; Oren Weimann

doi:10.1007/11575832_40

Normalized similarity of RNA sequences

Rolf Backofen, Danny Hermelin, Gad M. Landau, Oren Weimann

Department of Computer Science

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

Abstract

We introduce a normalized version of the LCS metric as a new local similarity measure for comparing two RNAs. An O(n²m lg m) time algorithm is presented for computing the maximum normalized score of two RNA sequences, where n and m are the lengths of the sequences and n ≤ m. This algorithm has the same time complexity as the currently best known global LCS algorithm.

Original language	English
Title of host publication	String Processing and Information Retrieval - 12th International Conference, SPIRE 2005, Proceedings
Pages	360-369
Number of pages	10
DOIs	https://doi.org/10.1007/11575832_40
State	Published - 2005
Event	12th International Conference on String Processing and Information Retrieval, SPIRE 2005 - Buenos Aires, Argentina Duration: 2 Nov 2005 → 4 Nov 2005

Publication series

Name	Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Volume	3772 LNCS
ISSN (Print)	0302-9743
ISSN (Electronic)	1611-3349

Conference

Conference	12th International Conference on String Processing and Information Retrieval, SPIRE 2005
Country/Territory	Argentina
City	Buenos Aires
Period	2/11/05 → 4/11/05

ASJC Scopus subject areas

Theoretical Computer Science
General Computer Science

Access to Document

10.1007/11575832_40

Cite this

Backofen, R., Hermelin, D., Landau, G. M., & Weimann, O. (2005). Normalized similarity of RNA sequences. In String Processing and Information Retrieval - 12th International Conference, SPIRE 2005, Proceedings (pp. 360-369). (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vol. 3772 LNCS). https://doi.org/10.1007/11575832_40

@inproceedings{00d899e37f9846d18d8d366188b2a5ba,

title = "Normalized similarity of RNA sequences",

abstract = "We introduce a normalized version of the LCS metric as a new local similarity measure for comparing two RNAs. An O(n2m lg m) time algorithm is presented for computing the maximum normalized score of two RNA sequences, where n and m are the lengths of the sequences and n ≤ m. This algorithm has the same time complexity as the currently best known global LCS algorithm.",

author = "Rolf Backofen and Danny Hermelin and Landau, {Gad M.} and Oren Weimann",

year = "2005",

doi = "10.1007/11575832_40",

language = "English",

isbn = "3540297405",

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

pages = "360--369",

booktitle = "String Processing and Information Retrieval - 12th International Conference, SPIRE 2005, Proceedings",

note = "12th International Conference on String Processing and Information Retrieval, SPIRE 2005 ; Conference date: 02-11-2005 Through 04-11-2005",

}

Backofen, R, Hermelin, D, Landau, GM & Weimann, O 2005, Normalized similarity of RNA sequences. in String Processing and Information Retrieval - 12th International Conference, SPIRE 2005, Proceedings. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), vol. 3772 LNCS, pp. 360-369, 12th International Conference on String Processing and Information Retrieval, SPIRE 2005, Buenos Aires, Argentina, 2/11/05. https://doi.org/10.1007/11575832_40

Normalized similarity of RNA sequences. / Backofen, Rolf; Hermelin, Danny; Landau, Gad M. et al.
String Processing and Information Retrieval - 12th International Conference, SPIRE 2005, Proceedings. 2005. p. 360-369 (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vol. 3772 LNCS).

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

TY - GEN

T1 - Normalized similarity of RNA sequences

AU - Backofen, Rolf

AU - Hermelin, Danny

AU - Landau, Gad M.

AU - Weimann, Oren

PY - 2005

Y1 - 2005

N2 - We introduce a normalized version of the LCS metric as a new local similarity measure for comparing two RNAs. An O(n2m lg m) time algorithm is presented for computing the maximum normalized score of two RNA sequences, where n and m are the lengths of the sequences and n ≤ m. This algorithm has the same time complexity as the currently best known global LCS algorithm.

AB - We introduce a normalized version of the LCS metric as a new local similarity measure for comparing two RNAs. An O(n2m lg m) time algorithm is presented for computing the maximum normalized score of two RNA sequences, where n and m are the lengths of the sequences and n ≤ m. This algorithm has the same time complexity as the currently best known global LCS algorithm.

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U2 - 10.1007/11575832_40

DO - 10.1007/11575832_40

M3 - Conference contribution

AN - SCOPUS:33646751901

SN - 3540297405

SN - 9783540297406

T3 - Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)

SP - 360

EP - 369

BT - String Processing and Information Retrieval - 12th International Conference, SPIRE 2005, Proceedings

T2 - 12th International Conference on String Processing and Information Retrieval, SPIRE 2005

Y2 - 2 November 2005 through 4 November 2005

ER -

Normalized similarity of RNA sequences

Abstract

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Conference

ASJC Scopus subject areas

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