Paper Info
Title
Analysis of internal loops within the RNA secondary structure in almost quadratic time
Abstract
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 O(M*log2L), ML2 is a number of possible nucleotide pairings. We created a software tool Afold which predicts the optimal secondary structure of RNA molecules of lengths up to 28 000 nt, using a computer with 2 Gb RAM. We also propose algorithms constructing sets of conditionally optimal multi-branch loop free (MLF) structures, e.g. the set that for every possible pairing (x, y) contains an optimal MLF structure in which nucleotides x and y form a pair. All the algorithms have run-time O(M*log2L). Availability: Executables of Afold software tool, precompiled for Linux and Windows, are available at ftp://ftp.ncbi.nlm.nih.gov/pub/ogurtsov/Afold. Contact: MRoytberg@impb.psn.ru Supplementary information: ftp://ftp.ncbi.nlm.nih.gov/pub/ogurtsov/Afold
Year
DOI
Venue
2006
10.1093/bioinformatics/btl083
Bioinformatics
Keywords
Field
DocType
bioinformatics,rna secondary structure,prediction,nucleotides,evaluation,secondary structure,loop group,rna
Data mining,Discrete mathematics,RNA,Computer science,Algorithm,Pairing,Software,Computer program,Loop group,Time complexity,Protein secondary structure,Nucleic acid secondary structure
Journal
Volume
Issue
ISSN
22
11
1367-4803
Citations 
PageRank 
References 
4
0.52
8
Authors
4
Name
Order
Citations
PageRank
Aleksey Y. Ogurtsov1414.42
S A Shabalina2425.55
A S Kondrashov3133.32
Mikhail A. Roytberg411454.66