An RNA structural motif searching tool. RNArobo can search sequence databases in FASTA format for a motif defined by a "descriptor", which can specify primary and secondary structure constraints.
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. http://dx.doi.org/10.1186/s12859-016-1074-x
tar -zxf rnarobo-2.1.0.tar.gzcd rnarobo-2.1.0/make
./rnarobo [options] <descriptor-file> <sequence-file>
e.g.: ./rnarobo -cu motif.des db.fa > occurrences.txt
-c search both strands of the database
-u report only non-overlapping occurrences
-f print output in plain FASTA format
-s print output in FASTA format with element separators
--nratio FLOAT set max allowed ratio of “N”s in reported occurrences to their length;
must be within <0,1>