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
- Current version of DotCodeR (github)
- DotcodeR (ver. 1.0.0) publication version
Please read the README.md file located in the DotCodeR directory for further instructions
Requirements
- ViennaRNA package (>= 2.0)
Data
- Training set for benchmarking DotcodeR
- Test set for benchmarking DotcodeR
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 | software ]
Contact
Yuki Kato Graduate School of Medicine, Osaka University, Japan
Jakob Hull Havgaard RTH, Faulty of Health and Medical Sciences, University of Copenhagen, Denmark