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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....
Autores principales: | , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2017
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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. |
format | Online Article Text |
id | pubmed-5712110 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2017 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
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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