Analysis of internal loops within the RNA secondary structure in almost quadratic time

Motivation: Evaluating all possible internal loops is one of the key steps in predicting the optimal secondary structure of an RNA molecule. The best algorithm available runs in time O(L3), L is the length of the RNA. Results: We propose a new algorithm for evaluating internal loops, its run-time is...

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Bibliographic Details

Published in:	Bioinformatics Vol. 22; no. 11; pp. 1317 - 1324
Main Authors:	Ogurtsov, Aleksey Y., Shabalina, Svetlana A., Kondrashov, Alexey S., Roytberg, Mikhail A.
Format:	Journal Article
Language:	English
Published:	England Oxford University Press 01.06.2006 Oxford Publishing Limited (England)
Subjects:	Algorithms Base Composition Computational Biology - methods Nucleic Acid Conformation Programming Languages RNA - chemistry Software Thermodynamics
ISSN:	1367-4803, 1460-2059, 1367-4811
Online Access:	Get full text
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