An RNA structural motif searching tool
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README.md

RNArobo

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

Compile RNArobo:

  • tar -zxf rnarobo-2.1.0.tar.gz
  • cd rnarobo-2.1.0/
  • make

Run RNArobo by the command:

./rnarobo [options] <descriptor-file> <sequence-file>
e.g.: ./rnarobo -cu motif.des db.fa > occurrences.txt

Available RNArobo Options:

-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>