RIsearch
This page is about RIsearch 1.x, for the suffix array-based RIsearch2 see here.
For more convenient use, add the installation folder to PATH or copy the binary to a location that is in $PATH, i.e.
With multiple sequences in fasta files, RIsearch does an all-against-all comparison.
Brief background
Regulatory, non-coding RNAs often function by duplex formation with other RNAs. Being able to predict these interactions in silico on a genome-wide scale is crucial to find possible targets for (and assign function to) ncRNA candidates, e.g. derived from computational screens. RIsearch is a program for fast RNA–RNA interaction search. It employs a modified Smith–Waterman–Gotoh algorithm based on di-nucleotides to approximate nearest-neighbor energy parameters.Get software
You can download the software here- 2014-04-23: Version 1.1 RIsearch-1.1.tar.gz
- 2013-01-11: Version 1.0 RIsearch-1.0.tar.gz
Installation
After download, unpack and compile with the following commands:tar -xzvf RIsearch-1.1.tar.gz cd RIsearch-1.1 makeThis will create a standalone executable 'RIsearch'.
For more convenient use, add the installation folder to PATH or copy the binary to a location that is in $PATH, i.e.
cp RIsearch /usr/local/bin/.
Usage
Required Parameters
RIsearch expects at least two parameters: query and target sequences, these can be given as fasta formatted files:RIsearch -q query.fa -t target.faor directly on the command line:
RIsearch -Q acguacgu -T cgauagcuguagacugaugcauA mixture of both is allowed as well.
With multiple sequences in fasta files, RIsearch does an all-against-all comparison.
Optional Parameters
-d <int> per-nucleotide extension penalty to favor short stable interactions, to be given in dacal/mol (recommended: 30, default: 0) -s <int> threshold for suboptimal duplexes (minimum score, NOT energy) -n <int> neighborhood (only backtrack from best position within this range - to omit many overlapping results); default is 0, backtrack all -l <int> max trace back length (default: 40) -m <str> scoring scheme to use, specify t99 to use the matrix based on Turner 1999 parameters (default is t04, Turner 2004) -e <num> energy threshold -p[123] switch for short output (one line per hit), different formatsFind more details and examples in the inlcuded README file.
Citation
When using this software, please cite:RIsearch: fast RNA-RNA interaction search using a simplified nearest-neighbor energy model
Wenzel A, Akbasli E, Gorodkin J
Bioinformatics. 2012 Nov 1;28(21):2738-46. Epub 2012 Aug 24
[ PubMed | Paper | Software ]