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Multiple Sequence Alignments Enhance Boundary Definition of RNA Structures

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Multiple Sequence Alignments Enhance Boundary Definition of RNA Structures. / Sabarinathan, Radhakrishnan; Anthon, Christian; Gorodkin, Jan; Seemann, Stefan E.

I: Genes, Bind 9, Nr. 12, 604, 04.12.2018.

Publikation: Bidrag til tidsskriftTidsskriftartikelForskningfagfællebedømt

Harvard

Sabarinathan, R, Anthon, C, Gorodkin, J & Seemann, SE 2018, 'Multiple Sequence Alignments Enhance Boundary Definition of RNA Structures', Genes, bind 9, nr. 12, 604. https://doi.org/10.3390/genes9120604

APA

Sabarinathan, R., Anthon, C., Gorodkin, J., & Seemann, S. E. (2018). Multiple Sequence Alignments Enhance Boundary Definition of RNA Structures. Genes, 9(12), [604]. https://doi.org/10.3390/genes9120604

Vancouver

Sabarinathan R, Anthon C, Gorodkin J, Seemann SE. Multiple Sequence Alignments Enhance Boundary Definition of RNA Structures. Genes. 2018 dec 4;9(12). 604. https://doi.org/10.3390/genes9120604

Author

Sabarinathan, Radhakrishnan ; Anthon, Christian ; Gorodkin, Jan ; Seemann, Stefan E. / Multiple Sequence Alignments Enhance Boundary Definition of RNA Structures. I: Genes. 2018 ; Bind 9, Nr. 12.

Bibtex

@article{f7927f7941e048f9a4c81feabc5b1892,
title = "Multiple Sequence Alignments Enhance Boundary Definition of RNA Structures",
abstract = "Self-contained structured domains of RNA sequences have often distinct molecular functions. Determining the boundaries of structured domains of a non-coding RNA (ncRNA) is needed for many ncRNA gene finder programs that predict RNA secondary structures in aligned genomes because these methods do not necessarily provide precise information about the boundaries or the location of the RNA structure inside the predicted ncRNA. Even without having a structure prediction, it is of interest to search for structured domains, such as for finding common RNA motifs in RNA-protein binding assays. The precise definition of the boundaries are essential for downstream analyses such as RNA structure modelling, e.g., through covariance models, and RNA structure clustering for the search of common motifs. Such efforts have so far been focused on single sequences, thus here we present a comparison for boundary definition between single sequence and multiple sequence alignments. We also present a novel approach, named RNAbound, for finding the boundaries that are based on probabilities of evolutionarily conserved base pairings. We tested the performance of two different methods on a limited number of Rfam families using the annotated structured RNA regions in the human genome and their multiple sequence alignments created from 14 species. The results show that multiple sequence alignments improve the boundary prediction for branched structures compared to single sequences independent of the chosen method. The actual performance of the two methods differs on single hairpin structures and branched structures. For the RNA families with branched structures, including transfer RNA (tRNA) and small nucleolar RNAs (snoRNAs), RNAbound improves the boundary predictions using multiple sequence alignments to median differences of -6 and -11.5 nucleotides (nts) for left and right boundary, respectively (window size of 200 nts).",
author = "Radhakrishnan Sabarinathan and Christian Anthon and Jan Gorodkin and Seemann, {Stefan E}",
year = "2018",
month = dec,
day = "4",
doi = "10.3390/genes9120604",
language = "English",
volume = "9",
journal = "Genes",
issn = "2073-4425",
publisher = "M D P I AG",
number = "12",

}

RIS

TY - JOUR

T1 - Multiple Sequence Alignments Enhance Boundary Definition of RNA Structures

AU - Sabarinathan, Radhakrishnan

AU - Anthon, Christian

AU - Gorodkin, Jan

AU - Seemann, Stefan E

PY - 2018/12/4

Y1 - 2018/12/4

N2 - Self-contained structured domains of RNA sequences have often distinct molecular functions. Determining the boundaries of structured domains of a non-coding RNA (ncRNA) is needed for many ncRNA gene finder programs that predict RNA secondary structures in aligned genomes because these methods do not necessarily provide precise information about the boundaries or the location of the RNA structure inside the predicted ncRNA. Even without having a structure prediction, it is of interest to search for structured domains, such as for finding common RNA motifs in RNA-protein binding assays. The precise definition of the boundaries are essential for downstream analyses such as RNA structure modelling, e.g., through covariance models, and RNA structure clustering for the search of common motifs. Such efforts have so far been focused on single sequences, thus here we present a comparison for boundary definition between single sequence and multiple sequence alignments. We also present a novel approach, named RNAbound, for finding the boundaries that are based on probabilities of evolutionarily conserved base pairings. We tested the performance of two different methods on a limited number of Rfam families using the annotated structured RNA regions in the human genome and their multiple sequence alignments created from 14 species. The results show that multiple sequence alignments improve the boundary prediction for branched structures compared to single sequences independent of the chosen method. The actual performance of the two methods differs on single hairpin structures and branched structures. For the RNA families with branched structures, including transfer RNA (tRNA) and small nucleolar RNAs (snoRNAs), RNAbound improves the boundary predictions using multiple sequence alignments to median differences of -6 and -11.5 nucleotides (nts) for left and right boundary, respectively (window size of 200 nts).

AB - Self-contained structured domains of RNA sequences have often distinct molecular functions. Determining the boundaries of structured domains of a non-coding RNA (ncRNA) is needed for many ncRNA gene finder programs that predict RNA secondary structures in aligned genomes because these methods do not necessarily provide precise information about the boundaries or the location of the RNA structure inside the predicted ncRNA. Even without having a structure prediction, it is of interest to search for structured domains, such as for finding common RNA motifs in RNA-protein binding assays. The precise definition of the boundaries are essential for downstream analyses such as RNA structure modelling, e.g., through covariance models, and RNA structure clustering for the search of common motifs. Such efforts have so far been focused on single sequences, thus here we present a comparison for boundary definition between single sequence and multiple sequence alignments. We also present a novel approach, named RNAbound, for finding the boundaries that are based on probabilities of evolutionarily conserved base pairings. We tested the performance of two different methods on a limited number of Rfam families using the annotated structured RNA regions in the human genome and their multiple sequence alignments created from 14 species. The results show that multiple sequence alignments improve the boundary prediction for branched structures compared to single sequences independent of the chosen method. The actual performance of the two methods differs on single hairpin structures and branched structures. For the RNA families with branched structures, including transfer RNA (tRNA) and small nucleolar RNAs (snoRNAs), RNAbound improves the boundary predictions using multiple sequence alignments to median differences of -6 and -11.5 nucleotides (nts) for left and right boundary, respectively (window size of 200 nts).

U2 - 10.3390/genes9120604

DO - 10.3390/genes9120604

M3 - Journal article

C2 - 30518121

VL - 9

JO - Genes

JF - Genes

SN - 2073-4425

IS - 12

M1 - 604

ER -

ID: 210016550