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

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

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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 languageEnglish
Title of host publicationProceedings Fifth International Conference on Intelligent Systems for Molecular Biology
Place of PublicationMenlo Park, CA, USA
PublisherAAAI Press
Publication date1997
Pages120-123
Publication statusPublished - 1997
Event5th International Conference on Intelligent Systems for Molecular Biology - Halkidiki, Greece
Duration: 21 Jun 199726 Jun 1997
Conference number: 5
http://www.aaai.org/Library/ISMB/ismb97contents.php

Conference

Conference5th International Conference on Intelligent Systems for Molecular Biology
Number5
CountryGreece
CityHalkidiki
Period21/06/199726/06/1997
Internet address

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