Skip Navigation

This Article
Right arrow Full Text (Print PDF)
Right arrow Alert me when this article is cited
Right arrow Alert me if a correction is posted
Services
Right arrow Email this article to a friend
Right arrow Similar articles in this journal
Right arrow Alert me to new issues of the journal
Right arrow Add to My Personal Archive
Right arrow Download to citation manager
Right arrowRequest Permissions
Google Scholar
Right arrow Articles by Chevalet, C.
Right arrow Articles by Michot, B.
Right arrow Search for Related Content
PubMed
Right arrow Articles by Chevalet, C.
Right arrow Articles by Michot, B.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

© Oxford University Press

An algorithm for comparing RNA secondary structures and searching for similar substructures

Claude Chevalet and Bernard Michot 1

Institut National de la Recherche Agronomique. Laboratoire de Génétique Cellulaire, chemin de Borde Rouge Auzeville BP 27, 31326 Castanet Tolosan Cedex
1Centre National de la Recherche Scientifique, Centre de Recherches de Biochimie et de Génétique Cellulaires 118 route de Narbonne, 31062 Toulouse Cedex, France

To access the functional informations carried by RNA molecules at the level of their secondary structure interactions, we propose a comparison method based on a tree edit algorithm which takes into account the tree structure of RNA foldings. Any secondary structure is translated into a tree involving all its elementary substructures; then a shorter condensed tree is built in which any unbranched helix interspersed with bulges and interior loops is taken as a single node. This method includes several parameters: a comparison matrix between structural units, gap penalties, and the scoring between nodes of the condensed trees. Their effects have been analysed using as a model a rapidly divergent domain of the large ribosomal RNA, for which structural lunation during evolution is well known. This method allows one to recognize precisely, in large target molecules, definite substructures that present with the query molecules only a limited set of closely related secondary structure features; it is still efficient if intervening features, which can correspond to insertion/deletion of entire stem regions, separate such structural elements. When coupled with a hierarchical clustering algorithm, this method is suitable for classifying RNA molecules according to their secondary structure homologies.

Received on June 18, 1991; accepted on November 26, 1991

Add to CiteULike CiteULike   Add to Connotea Connotea   Add to Del.icio.us Del.icio.us    What's this?


This article has been cited by other articles:


Home page
 Nucleic Acids ResHome page
S. Pasquali, H. H. Gan, and T. Schlick
Modular RNA architecture revealed by computational analysis of existing pseudoknots and ribosomal RNAs
Nucleic Acids Res., March 3, 2005; 33(4): 1384 - 1398.
[Abstract] [Full Text] [PDF]


Disclaimer:
Please note that abstracts for content published before 1996 were created through digital scanning and may therefore not exactly replicate the text of the original print issues. All efforts have been made to ensure accuracy, but the Publisher will not be held responsible for any remaining inaccuracies. If you require any further clarification, please contact our Customer Services Department.