Genomic screen for structured RNAs using coarse-grained secondary structure dot plots

Last modified: 2017-12-04

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. 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. DotcodeR can be useful as a pre-filter in a genomic comparative scan for structured RNAs.

Software download

Please read the README.md file located in the DotCodeR directory for further instructions

Requirements

Data

Reference

Alignment-free comparative genomic screen for structured RNAs using coarse-grained secondary structure dot plots
Yuki Kato, Jan Gorodkin and Jakob Hull Havgaard,
BMC Genomics 2017 18:935
[ pubmed | paper ]

Contact

Yuki Kato Graduate School of Medicine, Osaka University, Japan
Jakob Hull Havgaard RTH, Faulty of Health and Medical Sciences, University of Copenhagen, Denmark