Sparse RNA folding: Time and space efficient algorithms

Rolf Backofen, Dekel Tsur, Shay Zakov, Michal Ziv-Ukelson

Research output: Chapter in Book/Report/Conference proceedingConference contributionpeer-review

23 Scopus citations

Abstract

The classical algorithm for RNA single strand folding requires O(n Z) time and O(n 2) space, where n denotes the length of the input sequence and Z is a sparsity parameter that satisfies n ≤ Z ≤ n 2. We show how to reduce the space complexity of this algorithm. The space reduction is based on the observation that some solutions for subproblems are not examined after a certain stage of the algorithm, and may be discarded from memory. This yields an O(nZ) time and O(Z) space algorithm, that outputs both the cardinality of the optimal folding as well as a corresponding secondary structure. The space-efficient approach also extends to the related RNA simultaneous alignment with folding problem, and can be applied to reduce the space complexity of the fastest algorithm for this problem from O(n 2 m 2+ Z̃) down to Z̃ where n and m denote the lengths of the input sequences to be aligned, and is a sparsity parameter that satisfies n m ≤Z̃ ≤ n 2 m 2. In addition, we also show how to speed up the base-pairing maximization variant of RNA single strand folding. The speed up is achieved by combining two independent existing techniques, which restrict the number of expressions that need to be examined in bottleneck computations of these algorithms. This yields an O(LZ) time and O(Z) space algorithm, where L denotes the maximum cardinality of a folding of the input sequence. Additional online supporting material may be found at: http://www.cs.bgu.ac.il/zakovs/ RNAfold/CPM09-supporting-material.pdf

Original languageEnglish
Title of host publicationCombinatorial Pattern Matching - 20th Annual Symposium, CPM 2009, Proceedings
Pages249-262
Number of pages14
DOIs
StatePublished - 9 Nov 2009
Event20th Annual Symposium on Combinatorial Pattern Matching, CPM 2009 - Lille, France
Duration: 22 Jun 200924 Jun 2009

Publication series

NameLecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Volume5577 LNCS
ISSN (Print)0302-9743
ISSN (Electronic)1611-3349

Conference

Conference20th Annual Symposium on Combinatorial Pattern Matching, CPM 2009
Country/TerritoryFrance
CityLille
Period22/06/0924/06/09

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