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A Method for RNA Structure Prediction Shows Evidence for Structure in lncRNAs
To compare the secondary structure profiles of RNA molecules we developed the CROSSalign method. CROSSalign is based on the combination of the Computational Recognition Of Secondary Structure (CROSS) algorithm to predict the RNA secondary structure profile at single-nucleotide resolution and the Dyn...
Autores principales: | , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Frontiers Media S.A.
2018
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6286970/ https://www.ncbi.nlm.nih.gov/pubmed/30560136 http://dx.doi.org/10.3389/fmolb.2018.00111 |
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author | Delli Ponti, Riccardo Armaos, Alexandros Marti, Stefanie Tartaglia, Gian Gaetano |
author_facet | Delli Ponti, Riccardo Armaos, Alexandros Marti, Stefanie Tartaglia, Gian Gaetano |
author_sort | Delli Ponti, Riccardo |
collection | PubMed |
description | To compare the secondary structure profiles of RNA molecules we developed the CROSSalign method. CROSSalign is based on the combination of the Computational Recognition Of Secondary Structure (CROSS) algorithm to predict the RNA secondary structure profile at single-nucleotide resolution and the Dynamic Time Warping (DTW) method to align profiles of different lengths. We applied CROSSalign to investigate the structural conservation of long non-coding RNAs such as XIST and HOTAIR as well as ssRNA viruses including HIV. CROSSalign performs pair-wise comparisons and is able to find homologs between thousands of matches identifying the exact regions of similarity between profiles of different lengths. In a pool of sequences with the same secondary structure CROSSalign accurately recognizes repeat A of XIST and domain D2 of HOTAIR and outperforms other methods based on covariance modeling. The algorithm is freely available at the webpage http://service.tartaglialab.com//new_submission/crossalign. |
format | Online Article Text |
id | pubmed-6286970 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2018 |
publisher | Frontiers Media S.A. |
record_format | MEDLINE/PubMed |
spelling | pubmed-62869702018-12-17 A Method for RNA Structure Prediction Shows Evidence for Structure in lncRNAs Delli Ponti, Riccardo Armaos, Alexandros Marti, Stefanie Tartaglia, Gian Gaetano Front Mol Biosci Molecular Biosciences To compare the secondary structure profiles of RNA molecules we developed the CROSSalign method. CROSSalign is based on the combination of the Computational Recognition Of Secondary Structure (CROSS) algorithm to predict the RNA secondary structure profile at single-nucleotide resolution and the Dynamic Time Warping (DTW) method to align profiles of different lengths. We applied CROSSalign to investigate the structural conservation of long non-coding RNAs such as XIST and HOTAIR as well as ssRNA viruses including HIV. CROSSalign performs pair-wise comparisons and is able to find homologs between thousands of matches identifying the exact regions of similarity between profiles of different lengths. In a pool of sequences with the same secondary structure CROSSalign accurately recognizes repeat A of XIST and domain D2 of HOTAIR and outperforms other methods based on covariance modeling. The algorithm is freely available at the webpage http://service.tartaglialab.com//new_submission/crossalign. Frontiers Media S.A. 2018-12-03 /pmc/articles/PMC6286970/ /pubmed/30560136 http://dx.doi.org/10.3389/fmolb.2018.00111 Text en Copyright © 2018 Delli Ponti, Armaos, Marti and Tartaglia. http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms. |
spellingShingle | Molecular Biosciences Delli Ponti, Riccardo Armaos, Alexandros Marti, Stefanie Tartaglia, Gian Gaetano A Method for RNA Structure Prediction Shows Evidence for Structure in lncRNAs |
title | A Method for RNA Structure Prediction Shows Evidence for Structure in lncRNAs |
title_full | A Method for RNA Structure Prediction Shows Evidence for Structure in lncRNAs |
title_fullStr | A Method for RNA Structure Prediction Shows Evidence for Structure in lncRNAs |
title_full_unstemmed | A Method for RNA Structure Prediction Shows Evidence for Structure in lncRNAs |
title_short | A Method for RNA Structure Prediction Shows Evidence for Structure in lncRNAs |
title_sort | method for rna structure prediction shows evidence for structure in lncrnas |
topic | Molecular Biosciences |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6286970/ https://www.ncbi.nlm.nih.gov/pubmed/30560136 http://dx.doi.org/10.3389/fmolb.2018.00111 |
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