The University of Southampton
University of Southampton Institutional Repository
Warning ePrints Soton is experiencing an issue with some file downloads not being available. We are working hard to fix this. Please bear with us.

HotKnots: heuristic prediction of RNA secondary structures including pseudoknots

HotKnots: heuristic prediction of RNA secondary structures including pseudoknots
HotKnots: heuristic prediction of RNA secondary structures including pseudoknots
We present HotKnots, a new heuristic algorithm for the prediction of RNA secondary structures including pseudoknots. Based on the simple idea of iteratively forming stable stems, our algorithm explores many alternative secondary structures, using a free energy minimization algorithm for pseudoknot free secondary structures to identify promising candidate stems. In an empirical evaluation of the algorithm with 43 sequences taken from the Pseudobase database and from the literature on pseudoknotted structures, we found that overall, in terms of the sensitivity and specificity of predictions, HotKnots outperforms the well-known Pseudoknots algorithm of Rivas and Eddy and the NUPACK algorithm of Dirks and Pierce, both based on dynamic programming approaches for limited classes of pseudoknotted structures. It also outperforms the heuristic Iterated Loop Matching algorithm of Ruan and colleagues, and in many cases gives better results than the genetic algorithm from the STAR package of van Batenburg and colleagues and the recent pknotsRG-mfe algorithm of Reeder and Giegerich. The HotKnots algorithm has been implemented in C/C++ and is available from http://www.cs.ubc.ca/labs/beta/Software/HotKnots.
1355-8382
1494-1504
Ren, Jihong
4e677a5b-2e90-4a2a-a602-94cb64c015ef
Rastegari, Baharak
6ba9e93c-53ba-4090-8f77-c1cb1568d7d1
Condon, Anne
a1c1e645-b4b0-4449-a18e-6e43a440cce8
Hoos, Holger H.
766823b1-d684-4630-90a0-0bb157fe7e22
Ren, Jihong
4e677a5b-2e90-4a2a-a602-94cb64c015ef
Rastegari, Baharak
6ba9e93c-53ba-4090-8f77-c1cb1568d7d1
Condon, Anne
a1c1e645-b4b0-4449-a18e-6e43a440cce8
Hoos, Holger H.
766823b1-d684-4630-90a0-0bb157fe7e22

Ren, Jihong, Rastegari, Baharak, Condon, Anne and Hoos, Holger H. (2005) HotKnots: heuristic prediction of RNA secondary structures including pseudoknots. RNA, 11 (10), 1494-1504. (doi:10.1261/rna.7284905).

Record type: Article

Abstract

We present HotKnots, a new heuristic algorithm for the prediction of RNA secondary structures including pseudoknots. Based on the simple idea of iteratively forming stable stems, our algorithm explores many alternative secondary structures, using a free energy minimization algorithm for pseudoknot free secondary structures to identify promising candidate stems. In an empirical evaluation of the algorithm with 43 sequences taken from the Pseudobase database and from the literature on pseudoknotted structures, we found that overall, in terms of the sensitivity and specificity of predictions, HotKnots outperforms the well-known Pseudoknots algorithm of Rivas and Eddy and the NUPACK algorithm of Dirks and Pierce, both based on dynamic programming approaches for limited classes of pseudoknotted structures. It also outperforms the heuristic Iterated Loop Matching algorithm of Ruan and colleagues, and in many cases gives better results than the genetic algorithm from the STAR package of van Batenburg and colleagues and the recent pknotsRG-mfe algorithm of Reeder and Giegerich. The HotKnots algorithm has been implemented in C/C++ and is available from http://www.cs.ubc.ca/labs/beta/Software/HotKnots.

This record has no associated files available for download.

More information

Published date: 1 October 2005

Identifiers

Local EPrints ID: 426393
URI: http://eprints.soton.ac.uk/id/eprint/426393
ISSN: 1355-8382
PURE UUID: 45dd5c39-a70e-4cf6-9fe0-175720b886b4
ORCID for Baharak Rastegari: ORCID iD orcid.org/0000-0002-0985-573X

Catalogue record

Date deposited: 27 Nov 2018 17:30
Last modified: 10 Nov 2021 03:56

Export record

Altmetrics

Contributors

Author: Jihong Ren
Author: Baharak Rastegari ORCID iD
Author: Anne Condon
Author: Holger H. Hoos

Download statistics

Downloads from ePrints over the past year. Other digital versions may also be available to download e.g. from the publisher's website.

View more statistics

Atom RSS 1.0 RSS 2.0

Contact ePrints Soton: eprints@soton.ac.uk

ePrints Soton supports OAI 2.0 with a base URL of http://eprints.soton.ac.uk/cgi/oai2

This repository has been built using EPrints software, developed at the University of Southampton, but available to everyone to use.

We use cookies to ensure that we give you the best experience on our website. If you continue without changing your settings, we will assume that you are happy to receive cookies on the University of Southampton website.

×