RNArobo
RNArobo is an RNA structural motif search tool. RNArobo can search sequence databases in FASTA format for a motif defined by a descriptor, which can specify primary and secondary structure constraints. The format of an RNArobo descriptor is an extension of the descriptor format used by RNABob (a search tool by S. Eddy), so that RNABob descriptors are compatible with RNArobo. Unlike RNABob, RNArobo enables you to allow nucleotide insertions in a structural element. RNArobo was developed in collaboration with the group of Andrej Luptak.
GitHub repository
- The newest version can be found here
- Manual with a brief description of RNA descriptor format
Supplementary software
- FoldFilter: A set of Perl scripts for filtering RNAbob / RNArobo output.
- Javascript editor for graphical editing of RNAbob and RNArobo descriptors in your browser (author: Peter Koza).
- Perl script for parsing RNAbob / RNArobo output to fasta format.
References
- Ladislav Rampasek, Randi M. Jimenez, Andrej Luptak, Tomas Vinar, Brona Brejova. RNA motif search with data-driven element ordering. BMC Bioinformatics, 17(1):216. 2016.
The main paper describing the algorithms used by RNArobo.
- Randi M. Jimenez, Ladislav Rampášek, Broňa Brejová, Tomáš Vinař, Andrej Lupták. Discovery of RNA Motifs Using a Computational Pipeline that Allows Insertions in Paired Regions and Filtering of Candidate Sequences. In Jörg S. Hartig, ed., Ribozymes: Methods and Protocols, 848 volume of Methods in Molecular Biology, chapter 10, pp. 145-158, 2012. Springer.
A book chapter illustrating the use of RNAbob and FoldFilter.
- Bachelor
thesis and master thesis of Ladislav Rampášek describing the RNArobo tool.
Archived versions of RNArobo
