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

TY - JOUR

T1 - Alignment-free comparative genomic screen for structured RNAs using coarse-grained secondary structure dot plots

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

U2 - 10.1186/s12864-017-4309-y

DO - 10.1186/s12864-017-4309-y

M3 - Journal article

C2 - 29197323

AN - SCOPUS:85036497780

SN - 1471-2164

VL - 18

JO - BMC Genomics

JF - BMC Genomics

IS - 1

M1 - 935

ER -