ExpaRNA-P
ExpaRNA-P enumerates exactly matching local sequence-structure patterns in RNAs with unknown structure, supporting full structural flexibility based on RNA secondary structure energy models (inheriting from the Vienna RNA package).
Furthermore, it performs very fast simultaneous alignment and folding of RNAs (think: “like LocARNA, but faster”), internally based on exact matching.
Going far beyond previous matching approaches – including the older tool ExpaRNA, ExpaRNA-P considers the entire ensemble of potential RNA secondary structures. In consequence, ExpaRNA-P simultaneously matches and folds the input RNA sequences, enabling the enumeration of thermodynamically relevant local sequence-structure motifs. This approach avoids committing to unreliable predicted single RNA structures.
ExpaRNA-P is distributed as part of the LocARNA package. Please find the download link to the latest release there. The software is freely available under GPL 3.0.
The software is tested on recent GNU/Linux systems. It is also reported to work under macOS or Windows Cygwin. Please follow the installation instructions provided with LocARNA.
exparna_pThe basic tool exparna_p computes Exact Pattern Matchings (EPMs) in the Boltzmann-distributed structure ensemble of two RNA sequences. The wrapper script exploc_p performs Simultaneous Matching and Folding (SM&F) of RNA sequences. The EPMs computed by exparna_p are used as anchor constraints to speed up alignment computation with locarna.
exparna_p expects two input files in FASTA format containing the first and second sequences, respectively:
fileA:
> seqA
... [Your first RNA sequence] ...
fileB:
> seqB
... [Your second RNA sequence] ...
Call exparna_p as follows:
exparna_p fileA fileB
By default, exparna_p computes all EPMs with a given minimal score using heuristic traceback. Several options are available to control the output:
--output-ps filename: Outputs best EPM chain as a colored PostScript.--output-epm-list filename: Outputs a list of all traced EPMs.--output-chained-epm-list filename: Outputs a list of all chained EPMs.Help for exparna_p options can be accessed via:
exparna_p --help
exparna_p --man
exploc_pThis script uses the best chain of EPMs from exparna_p as anchor constraints for locarna. It expects two input files in FASTA format:
fileA:
> seqA
... [Your first RNA sequence] ...
fileB:
> seqB
... [Your second RNA sequence] ...
Call exploc_p as follows:
exploc_p fileA fileB
The program writes anchor constraints to the current directory. You can control the output directory using the --output option. Help for exploc_p options can be accessed via:
exploc_p --help
exploc_p --man
Christina Otto, Mathias Mohl, Steffen Heyne, Mika Amit, Gad M. Landau, Rolf Backofen, and Sebastian Will ExpaRNA-P: simultaneous exact pattern matching and folding of RNAs BMC Bioinformatics, 15 no. 1 pp. 6602, 2014.