Finding Common Sequence and Structure Motifs in a set of RNA
                sequences

Jan Gorodkin; Laurie J. Heyer; Gary D. Stormo

Finding Common Sequence and Structure Motifs in a set of RNA sequences

Jan Gorodkin, Laurie J. Heyer, Gary D. Stormo

Department of Chemistry

University of Colorado

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

Abstract

We present a computational scheme to search for the most common motif, composed of a combination of sequence and structure constraints, among a collection of RNA sequences. The method uses a simplified version of the Sankoff algorithm for simultaneous folding and alignment of RNA sequences, but maintains tractability by constructing multi-sequence alignments for pairwise comparisons. The overall method has similarities to both CLUSTAL and CONSENSUS, but the core algorithm assures that the pairwise alignments are optimized for both sequence and structure conservation. Example solutions, and comparisons with other approaches, are provided. The solutions include finding consensus structure identical to published ones.

Original language	English
Title of host publication	Proceedings Fifth International Conference on Intelligent Systems for Molecular Biology
Place of Publication	Menlo Park, CA, USA
Publisher	AAAI Press
Publication date	1997
Pages	120-123
Publication status	Published - 1997
Event	5th International Conference on Intelligent Systems for Molecular Biology - Halkidiki, Greece Duration: 21 Jun 1997 → 26 Jun 1997 Conference number: 5 http://www.aaai.org/Library/ISMB/ismb97contents.php

Conference

Conference	5th International Conference on Intelligent Systems for Molecular Biology
Number	5
Country/Territory	Greece
City	Halkidiki
Period	21/06/1997 → 26/06/1997
Internet address	http://www.aaai.org/Library/ISMB/ismb97contents.php

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Cite this

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title = "Finding Common Sequence and Structure Motifs in a set of RNA sequences",

abstract = "We present a computational scheme to search for the most common motif, composed of a combination of sequence and structure constraints, among a collection of RNA sequences. The method uses a simplified version of the Sankoff algorithm for simultaneous folding and alignment of RNA sequences, but maintains tractability by constructing multi-sequence alignments for pairwise comparisons. The overall method has similarities to both CLUSTAL and CONSENSUS, but the core algorithm assures that the pairwise alignments are optimized for both sequence and structure conservation. Example solutions, and comparisons with other approaches, are provided. The solutions include finding consensus structure identical to published ones.",

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publisher = "AAAI Press",

note = "5th International Conference on Intelligent Systems for Molecular Biology ; Conference date: 21-06-1997 Through 26-06-1997",

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Gorodkin, J, Heyer, LJ & Stormo, GD 1997, Finding Common Sequence and Structure Motifs in a set of RNA sequences. in Proceedings Fifth International Conference on Intelligent Systems for Molecular Biology. AAAI Press, Menlo Park, CA, USA, pp. 120-123, 5th International Conference on Intelligent Systems for Molecular Biology, Halkidiki, Greece, 21/06/1997.

Finding Common Sequence and Structure Motifs in a set of RNA sequences. / Gorodkin, Jan; Heyer, Laurie J.; Stormo, Gary D.

Proceedings Fifth International Conference on Intelligent Systems for Molecular Biology. Menlo Park, CA, USA : AAAI Press, 1997. p. 120-123.

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

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AU - Heyer, Laurie J.

AU - Stormo, Gary D.

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PY - 1997

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N2 - We present a computational scheme to search for the most common motif, composed of a combination of sequence and structure constraints, among a collection of RNA sequences. The method uses a simplified version of the Sankoff algorithm for simultaneous folding and alignment of RNA sequences, but maintains tractability by constructing multi-sequence alignments for pairwise comparisons. The overall method has similarities to both CLUSTAL and CONSENSUS, but the core algorithm assures that the pairwise alignments are optimized for both sequence and structure conservation. Example solutions, and comparisons with other approaches, are provided. The solutions include finding consensus structure identical to published ones.

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M3 - Article in proceedings

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BT - Proceedings Fifth International Conference on Intelligent Systems for Molecular Biology

PB - AAAI Press

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