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RNAcode - Analyze the protein coding potential in multiple sequence alignments

RNAcode predicts protein coding regions in a a set of homologous nucleotide sequences. RNAcode relies on evolutionary signatures including synonymous/conservative mutations and conservation of the reading frame. It does not use any species specific sequence characteristics whatsoever and does not use any machine learning techniques.

RNAcode is designed to work "out-of-the box" to give answers quickly. The only input required for RNAcode is a multiple sequence alignment either in MAF or Clustal W format. RNAcode reports local regions with high coding potential, an associated p-value and a color annotation of mutational patterns.

Download & Install

Download source code distribution of RNAcode: RNAcode-0.3.tar.gz

Extract the file and run:

make install
See file INSTALL for details.

RNAcode is licenced under The GNU General Public License version 3.

You can get the code at Github by running:

$ git clone git://


RNAcode: robust discrimination of coding and noncoding regions in comparative sequence data.
Washietl S, Findeiss S, Müller SA, Kalkhof S, von Bergen M, Hofacker IL, Stadler PF, Goldman N.
RNA. 2011;17(4):578-94.


Stefan Washietl