Automated identification of RNA 3D modules with discriminative power in RNA structural alignments

Recent progress in predicting RNA structure is moving towards filling the ‘gap’ in 2D RNA structure prediction where, for example, predicted internal loops often form non-canonical base pairs. This is increasingly recognized with the steady increase of known RNA 3D modules. There is a general intere...

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Main Authors:	Theis, Corinna, Höner zu Siederdissen, Christian, Hofacker, Ivo L., Gorodkin, Jan
Format:	Online
Language:	English
Published:	Oxford University Press 2013
Online Access:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3905863/

id	pubmed-3905863
recordtype	oai_dc
spelling	pubmed-39058632014-01-29 Automated identification of RNA 3D modules with discriminative power in RNA structural alignments Theis, Corinna Höner zu Siederdissen, Christian Hofacker, Ivo L. Gorodkin, Jan Computational Biology Recent progress in predicting RNA structure is moving towards filling the ‘gap’ in 2D RNA structure prediction where, for example, predicted internal loops often form non-canonical base pairs. This is increasingly recognized with the steady increase of known RNA 3D modules. There is a general interest in matching structural modules known from one molecule to other molecules for which the 3D structure is not known yet. We have created a pipeline, metaRNAmodules, which completely automates extracting putative modules from the FR3D database and mapping of such modules to Rfam alignments to obtain comparative evidence. Subsequently, the modules, initially represented by a graph, are turned into models for the RMDetect program, which allows to test their discriminative power using real and randomized Rfam alignments. An initial extraction of 22 495 3D modules in all PDB files results in 977 internal loop and 17 hairpin modules with clear discriminatory power. Many of these modules describe only minor variants of each other. Indeed, mapping of the modules onto Rfam families results in 35 unique locations in 11 different families. The metaRNAmodules pipeline source for the internal loop modules is available at http://rth.dk/resources/mrm. Oxford University Press 2013-12 2013-09-04 /pmc/articles/PMC3905863/ /pubmed/24005040 http://dx.doi.org/10.1093/nar/gkt795 Text en © The Author(s) 2013. Published by Oxford University Press. http://creativecommons.org/licenses/by-nc/3.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/3.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com
repository_type	Open Access Journal
institution_category	Foreign Institution
institution	US National Center for Biotechnology Information
building	NCBI PubMed
collection	Online Access
language	English
format	Online
author	Theis, Corinna Höner zu Siederdissen, Christian Hofacker, Ivo L. Gorodkin, Jan
spellingShingle	Theis, Corinna Höner zu Siederdissen, Christian Hofacker, Ivo L. Gorodkin, Jan Automated identification of RNA 3D modules with discriminative power in RNA structural alignments
author_facet	Theis, Corinna Höner zu Siederdissen, Christian Hofacker, Ivo L. Gorodkin, Jan
author_sort	Theis, Corinna
title	Automated identification of RNA 3D modules with discriminative power in RNA structural alignments
title_short	Automated identification of RNA 3D modules with discriminative power in RNA structural alignments
title_full	Automated identification of RNA 3D modules with discriminative power in RNA structural alignments
title_fullStr	Automated identification of RNA 3D modules with discriminative power in RNA structural alignments
title_full_unstemmed	Automated identification of RNA 3D modules with discriminative power in RNA structural alignments
title_sort	automated identification of rna 3d modules with discriminative power in rna structural alignments
description	Recent progress in predicting RNA structure is moving towards filling the ‘gap’ in 2D RNA structure prediction where, for example, predicted internal loops often form non-canonical base pairs. This is increasingly recognized with the steady increase of known RNA 3D modules. There is a general interest in matching structural modules known from one molecule to other molecules for which the 3D structure is not known yet. We have created a pipeline, metaRNAmodules, which completely automates extracting putative modules from the FR3D database and mapping of such modules to Rfam alignments to obtain comparative evidence. Subsequently, the modules, initially represented by a graph, are turned into models for the RMDetect program, which allows to test their discriminative power using real and randomized Rfam alignments. An initial extraction of 22 495 3D modules in all PDB files results in 977 internal loop and 17 hairpin modules with clear discriminatory power. Many of these modules describe only minor variants of each other. Indeed, mapping of the modules onto Rfam families results in 35 unique locations in 11 different families. The metaRNAmodules pipeline source for the internal loop modules is available at http://rth.dk/resources/mrm.
publisher	Oxford University Press
publishDate	2013
url	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3905863/
_version_	1612052474529579008

Automated identification of RNA 3D modules with discriminative power in RNA structural alignments

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