MXSCARNA (Multiplex Stem Candidate Aligner for RNAs) is a tool for fast structural multiple alignment of RNA sequences using progressive alignment based on pairwise structural alignment algorithm of SCARNA.


While its original source code is provided as free software, MXSCARNA contains the source codes of ProbCons and Rfold and the energy parameters of Vienna RNA package (version 1.5). The author thanks Dr. Chuong Do, Dr. Hisanori Kiryu and Dr. Ivo Hofacker, the authors of ProbCons, Rfold and Vienna RNA package respectively,and Institute for Theoretical Chemistry of the University of Vienna.

The source code of Rfold is located in ./src/rfold-0.1, which includes energy parameters of Vienna RNA package in ./src/rfold-0.1/src/vienna. Energy parameters of Vienna RNA package are also included in the source code of MXSCARNA (./src/vienna). Please follow ./src/rfold-0.1/readme.txt file, which describes the license of Rfold, and ./src/rfold-0.1/src/vienna/COPYING file and ./src/vienna/COPYING file, which describe the copyright notice of the Vienna RNA package. The source code of ProbCons is located in ./src/probconsRNA. Please follow ./src/probcons/README.

The original part of MXSCARNA is provided as free software.

It is distributed in the hope that it will be useful but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.

Permission is granted for research, educational, and commercial use and modification so long as
1) the package and any derived works are not redistributed for any fee, other than media costs,
2) proper credit is given to the authors of MXSCARNA, ProbCons, Rfold and Vienna RNA package, the Univeristy of Tokyo,
Computational Biology Research Center (CBRC), AIST and Institute for Theoretical Chemistry of the University of Vienna.

If you want to include this software in a commercial product, please contact the author.


A new version of MXSCARNA has been released.

mxscarna_ver2.1_060309.tar.gz (3 MB)

If you have a compile trouble, please try to use the following version.

mxscarna_ver1.9.tar.gz (539 KB)


2009-03-06: A compile error has been fixed.
2008-06-09: mxscarna ver2.1 release
– A compile error has been fixed.

2008-05-27: mxscarna_ver1.9 release
– This version do not include Rfold.

2008-01-16: mxscarna ver2.0 release
– The source code of MXSCARNA is downloadable.Rfold was incorporated to calculate local base paring probability matrices.

  • 2007-11-24: mxscarna ver1.3 release


The program was tested using gcc 3.3.3 on linux machines and gcc 3.4 on cygwin.
Some gcc specific features are currently used.

The command to compile this software is as follows:

cd program


./mxscarna [options]

: sequence file in multi fasta format

use CLUSTALW output format instead of MFA

use STOCKHOLM output format instead of MFA

use original output format instead of MFA

the length of stem candidates (default:2)

the threshold of base-pairing probability (default:0.01)

the control parameter of the prediction of base-pairs, (default:6)

use Rfold instead of global McCaskill algorithm to calculate base pairing
probability matrices, (default: off)

the control parameter of the distance of stem candidates, (default: 500)


./mxscarna -mxscarna ../sample/trna.mfa


Yasuo Tabei, Hisanori Kiryu, Taishin Kin and Kiyoshi Asai,
A fast structural alignment method for long RNA sequences
BMC Bioinformatics 2008, 9:33 (23 January 2008)

Do, C.B., Mahabhashyam, M.S.P., Brudno, M., and Batzoglou, S. 2005.
PROBCONS: Probabilistic Consistency-based Multiple Sequence Alignment.
Genome Research 15: 330-340.

Hisanori Kiryu, Taishin Kin, and Kiyoshi Asai
Rfold: An exact algorithm for computing local base pairing probabilities
Bioinformatics, Advance Access published on December 4, 2007; doi:10.1093/bioinformatics/btm591

Ivo L. Hofacker
Vienna RNA secondary structure server
Nucleic Acids Res., Jul 2003; 31: 3429 – 3431.

Yasuo Tabei, Koji Tsuda, Taishin Kin, and Kiyoshi Asai
SCARNA: fast and accurate structural alignment of RNA sequences by matching fixed-length stem fragments
Bioinformatics 2006 22(14):1723-1729.