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Alignment-free comparative genomic screen for structured RNAs using coarse-grained secondary structure dot plots

BACKGROUND: Structured non-coding RNAs play many different roles in the cells, but the annotation of these RNAs is lacking even within the human genome. The currently available computational tools are either too computationally heavy for use in full genomic screens or rely on pre-aligned sequences....

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Detalles Bibliográficos
Autores principales: Kato, Yuki, Gorodkin, Jan, Havgaard, Jakob Hull
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2017
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5712110/
https://www.ncbi.nlm.nih.gov/pubmed/29197323
http://dx.doi.org/10.1186/s12864-017-4309-y
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author Kato, Yuki
Gorodkin, Jan
Havgaard, Jakob Hull
author_facet Kato, Yuki
Gorodkin, Jan
Havgaard, Jakob Hull
author_sort Kato, Yuki
collection PubMed
description BACKGROUND: Structured non-coding RNAs play many different roles in the cells, but the annotation of these RNAs is lacking even within the human genome. The currently available computational tools are either too computationally heavy for use in full genomic screens or rely on pre-aligned sequences. METHODS: Here we present a fast and efficient method, DotcodeR, for detecting structurally similar RNAs in genomic sequences by comparing their corresponding coarse-grained secondary structure dot plots at string level. This allows us to perform an all-against-all scan of all window pairs from two genomes without alignment. RESULTS: Our computational experiments with simulated data and real chromosomes demonstrate that the presented method has good sensitivity. CONCLUSIONS: DotcodeR can be useful as a pre-filter in a genomic comparative scan for structured RNAs. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12864-017-4309-y) contains supplementary material, which is available to authorized users.
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spelling pubmed-57121102017-12-06 Alignment-free comparative genomic screen for structured RNAs using coarse-grained secondary structure dot plots Kato, Yuki Gorodkin, Jan Havgaard, Jakob Hull BMC Genomics Methodology Article BACKGROUND: Structured non-coding RNAs play many different roles in the cells, but the annotation of these RNAs is lacking even within the human genome. The currently available computational tools are either too computationally heavy for use in full genomic screens or rely on pre-aligned sequences. METHODS: Here we present a fast and efficient method, DotcodeR, for detecting structurally similar RNAs in genomic sequences by comparing their corresponding coarse-grained secondary structure dot plots at string level. This allows us to perform an all-against-all scan of all window pairs from two genomes without alignment. RESULTS: Our computational experiments with simulated data and real chromosomes demonstrate that the presented method has good sensitivity. CONCLUSIONS: DotcodeR can be useful as a pre-filter in a genomic comparative scan for structured RNAs. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12864-017-4309-y) contains supplementary material, which is available to authorized users. BioMed Central 2017-12-02 /pmc/articles/PMC5712110/ /pubmed/29197323 http://dx.doi.org/10.1186/s12864-017-4309-y Text en © The Author(s) 2017 Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
spellingShingle Methodology Article
Kato, Yuki
Gorodkin, Jan
Havgaard, Jakob Hull
Alignment-free comparative genomic screen for structured RNAs using coarse-grained secondary structure dot plots
title Alignment-free comparative genomic screen for structured RNAs using coarse-grained secondary structure dot plots
title_full Alignment-free comparative genomic screen for structured RNAs using coarse-grained secondary structure dot plots
title_fullStr Alignment-free comparative genomic screen for structured RNAs using coarse-grained secondary structure dot plots
title_full_unstemmed Alignment-free comparative genomic screen for structured RNAs using coarse-grained secondary structure dot plots
title_short Alignment-free comparative genomic screen for structured RNAs using coarse-grained secondary structure dot plots
title_sort alignment-free comparative genomic screen for structured rnas using coarse-grained secondary structure dot plots
topic Methodology Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5712110/
https://www.ncbi.nlm.nih.gov/pubmed/29197323
http://dx.doi.org/10.1186/s12864-017-4309-y
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