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

Yuki Kato; Jan Gorodkin; Jakob Hull Havgaard

doi:10.1186/s12864-017-4309-y

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

Yuki Kato^*, Jan Gorodkin, Jakob Hull Havgaard

^*Corresponding author for this work

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Abstract

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.

Original language	English
Article number	935
Journal	BMC Genomics
Volume	18
Issue number	1
ISSN	1471-2164
DOIs	https://doi.org/10.1186/s12864-017-4309-y
Publication status	Published - Dec 2017

Keywords

Gene finding
Non-coding RNA
Secondary structure

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10.1186/s12864-017-4309-yLicence: CC BY

Alignment-free comparative genomic screen for structured RNAs using coarse-grained secondary structure dot plotsFinal published version, 663 KBLicence: CC BY

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

abstract = "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.",

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AU - Kato, Yuki

AU - Gorodkin, Jan

AU - Havgaard, Jakob Hull

PY - 2017/12

Y1 - 2017/12

N2 - 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.

AB - 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.

KW - Gene finding

KW - Non-coding RNA

KW - Secondary structure

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DO - 10.1186/s12864-017-4309-y

M3 - Journal article

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JO - BMC Genomics

JF - BMC Genomics

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ER -

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

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Keywords

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