Local exact pattern matching for non-fixed RNA structures

Mika Amit; Rolf Backofen; Steffen Heyne; Gad M. Landau; Mathias Möhl; Christina Schmiedl; Sebastian Will

doi:10.1007/978-3-642-31265-6_25

Local exact pattern matching for non-fixed RNA structures

Mika Amit, Rolf Backofen, Steffen Heyne, Gad M. Landau, Mathias Möhl, Christina Schmiedl, Sebastian Will

Department of Computer Science

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

Abstract

Detecting local common sequence-structure regions of RNAs is a biologically meaningful problem. By detecting such regions, biologists are able to identify functional similarity between the inspected molecules. We developed dynamic programming algorithms for finding common structure-sequence patterns between two RNAs. The RNAs are given by their sequence and a set of potential base pairs with associated probabilities. In contrast to prior work which matches fixed structures, we support the arc breaking edit operation; this allows to match only a subset of the given base pairs. We present an O(n ³) algorithm for local exact pattern matching between two nested RNAs, and an O(n ³logn) algorithm for one nested RNA and one bounded-unlimited RNA.

Original language	English
Title of host publication	Combinatorial Pattern Matching - 23rd Annual Symposium, CPM 2012, Proceedings
Pages	306-320
Number of pages	15
DOIs	https://doi.org/10.1007/978-3-642-31265-6_25
State	Published - 2012
Event	23rd Annual Symposium on Combinatorial Pattern Matching, CPM 2012 - Helsinki, Finland Duration: 3 Jul 2012 → 5 Jul 2012

Publication series

Name	Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Volume	7354 LNCS
ISSN (Print)	0302-9743
ISSN (Electronic)	1611-3349

Conference

Conference	23rd Annual Symposium on Combinatorial Pattern Matching, CPM 2012
Country/Territory	Finland
City	Helsinki
Period	3/07/12 → 5/07/12

ASJC Scopus subject areas

Theoretical Computer Science
General Computer Science

Access to Document

10.1007/978-3-642-31265-6_25

Cite this

Amit, M., Backofen, R., Heyne, S., Landau, G. M., Möhl, M., Schmiedl, C., & Will, S. (2012). Local exact pattern matching for non-fixed RNA structures. In Combinatorial Pattern Matching - 23rd Annual Symposium, CPM 2012, Proceedings (pp. 306-320). (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vol. 7354 LNCS). https://doi.org/10.1007/978-3-642-31265-6_25

@inproceedings{c0e1e12bdbc748ab90ba9c688c463b62,

title = "Local exact pattern matching for non-fixed RNA structures",

abstract = "Detecting local common sequence-structure regions of RNAs is a biologically meaningful problem. By detecting such regions, biologists are able to identify functional similarity between the inspected molecules. We developed dynamic programming algorithms for finding common structure-sequence patterns between two RNAs. The RNAs are given by their sequence and a set of potential base pairs with associated probabilities. In contrast to prior work which matches fixed structures, we support the arc breaking edit operation; this allows to match only a subset of the given base pairs. We present an O(n 3) algorithm for local exact pattern matching between two nested RNAs, and an O(n 3logn) algorithm for one nested RNA and one bounded-unlimited RNA.",

author = "Mika Amit and Rolf Backofen and Steffen Heyne and Landau, {Gad M.} and Mathias M{\"o}hl and Christina Schmiedl and Sebastian Will",

year = "2012",

doi = "10.1007/978-3-642-31265-6_25",

language = "English",

isbn = "9783642312649",

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

pages = "306--320",

booktitle = "Combinatorial Pattern Matching - 23rd Annual Symposium, CPM 2012, Proceedings",

note = "23rd Annual Symposium on Combinatorial Pattern Matching, CPM 2012 ; Conference date: 03-07-2012 Through 05-07-2012",

}

Amit, M, Backofen, R, Heyne, S, Landau, GM, Möhl, M, Schmiedl, C & Will, S 2012, Local exact pattern matching for non-fixed RNA structures. in Combinatorial Pattern Matching - 23rd Annual Symposium, CPM 2012, Proceedings. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), vol. 7354 LNCS, pp. 306-320, 23rd Annual Symposium on Combinatorial Pattern Matching, CPM 2012, Helsinki, Finland, 3/07/12. https://doi.org/10.1007/978-3-642-31265-6_25

Local exact pattern matching for non-fixed RNA structures. / Amit, Mika; Backofen, Rolf; Heyne, Steffen et al.
Combinatorial Pattern Matching - 23rd Annual Symposium, CPM 2012, Proceedings. 2012. p. 306-320 (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vol. 7354 LNCS).

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

TY - GEN

T1 - Local exact pattern matching for non-fixed RNA structures

AU - Amit, Mika

AU - Backofen, Rolf

AU - Heyne, Steffen

AU - Landau, Gad M.

AU - Möhl, Mathias

AU - Schmiedl, Christina

AU - Will, Sebastian

PY - 2012

Y1 - 2012

N2 - Detecting local common sequence-structure regions of RNAs is a biologically meaningful problem. By detecting such regions, biologists are able to identify functional similarity between the inspected molecules. We developed dynamic programming algorithms for finding common structure-sequence patterns between two RNAs. The RNAs are given by their sequence and a set of potential base pairs with associated probabilities. In contrast to prior work which matches fixed structures, we support the arc breaking edit operation; this allows to match only a subset of the given base pairs. We present an O(n 3) algorithm for local exact pattern matching between two nested RNAs, and an O(n 3logn) algorithm for one nested RNA and one bounded-unlimited RNA.

AB - Detecting local common sequence-structure regions of RNAs is a biologically meaningful problem. By detecting such regions, biologists are able to identify functional similarity between the inspected molecules. We developed dynamic programming algorithms for finding common structure-sequence patterns between two RNAs. The RNAs are given by their sequence and a set of potential base pairs with associated probabilities. In contrast to prior work which matches fixed structures, we support the arc breaking edit operation; this allows to match only a subset of the given base pairs. We present an O(n 3) algorithm for local exact pattern matching between two nested RNAs, and an O(n 3logn) algorithm for one nested RNA and one bounded-unlimited RNA.

UR - http://www.scopus.com/inward/record.url?scp=84863104682&partnerID=8YFLogxK

U2 - 10.1007/978-3-642-31265-6_25

DO - 10.1007/978-3-642-31265-6_25

M3 - Conference contribution

AN - SCOPUS:84863104682

SN - 9783642312649

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

SP - 306

EP - 320

BT - Combinatorial Pattern Matching - 23rd Annual Symposium, CPM 2012, Proceedings

T2 - 23rd Annual Symposium on Combinatorial Pattern Matching, CPM 2012

Y2 - 3 July 2012 through 5 July 2012

ER -

Amit M, Backofen R, Heyne S, Landau GM, Möhl M, Schmiedl C et al. Local exact pattern matching for non-fixed RNA structures. In Combinatorial Pattern Matching - 23rd Annual Symposium, CPM 2012, Proceedings. 2012. p. 306-320. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)). doi: 10.1007/978-3-642-31265-6_25

Local exact pattern matching for non-fixed RNA structures

Abstract

Publication series

Conference

ASJC Scopus subject areas

Access to Document

Other files and links

Fingerprint

Cite this