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-1.Program name
- MXSCARNA
-
-2.Author
- Yasuo Tabei
-
- Department of Computational Biology,
- Graduate School of Frontier Science,
- The University of Tokyo
- and
- Computational Biology Research Center (CBRC),
- National Institute of Advanced Industrial Science and Technology (AIST)
-
- E-mail: scarna@m.aist.go.jp
-
-3.What is MXSCARNA
- 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.
-
-4.License
- 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.
-
-5.Citation
- Yasuo Tabei, Hisanori Kiryu, Taishin Kin, Kiyoshi Asai:
- "A fast structural multiple alignment method for long RNA sequences,"
- BMC bioinformatics, to appear.
-
-6.References
-
- 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.
-
-7.Install
- 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:
-
- make
- cd program
-
-8.Usage
-
- ./mxscarna [options] seqfile
-
- seqfile:
- sequence file is multi fasta format.
-
- options:
- -clustalw
- use CLUSTALW output format instead of MFA
-
- -stockholm
- use STOCKHOLM output format instead of MFA
-
- -mxscarna
- use original output format instead of MFA
-
- -l <SCSLENGTH>
- the length of stem candidates (default:2)
-
- -b <BASEPROBTHRESHOLD>
- the threshold of base-pairing probability (default:0.01)
-
- -g <BASEPAIRSCORECONT>
- the control parameter of the prediction of base-pairs, (default:6)
-
- -rfold
- use Rfold instead of global McCaskill algorithm to calcurate base
- paring probality matrices, (default: off)
-
- -w <BANDWIDTH>
- the control parameter of the distance of stem candidates, (default:500)
-
-9.Example
- ./mxscarna -mxscarna ../sample/trna.mfa
-
-10.Version History
-1. 1/16/2008 (Yasuo Tabei)
--- MXSCARNA ver 2.0 release
- - Rfold was included.
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git://source.jalview.org / jabaws.git / blobdiff