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A local multiple alignment method for detection of non-coding RNA sequences
Introduction
SCARNA_LM (SCARNA Local Multiple) is a local multiple aligner for RNA sequences.It is based on a discriminative pairwise alignment model which incorporates secondary structure features as base pairing probability calcurated by Rfold, and uses an efficient local multiple alignment constrction procedure proposed By Phuong et al for local multiple alignments of protein sequences. As postprocessing, it calcurates global multiple alignments via MXSCARNA.
License
While its original source code is provided as free software, SCARNA_LM contains
the source codes of ProDA, Contralign, Rfold and the energy parameters of Vienna RNA
package (version 1.5). The author thanks Dr. Tu Minh Phuong, Dr. Chuong B. Do,
Dr Hisanori Kiryu, Dr. Ivo Hofacker, the authors of ProDA, Contralign, Rfold
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 ./src/McCaskill/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/McCaskill/vienna/COPYING file,
which describe the copyright notice of the Vienna RNA package.
The source code of Conralign is located in ./src/Model. Please follow ./src/Model/README.
The souce code of ProDA is located in ./src/proda.
The original part of SCARNA_LM 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 SCARNA_LM, ProDA, Contralign, 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.
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News
- 2009-05-15: SCARNA_LM ver2.2
- SCARNA_LM ver2.2 has been released.
- 2009-04-30: SCARNA_LM ver2.1
- SCARNA_LM ver2.1 has been released.
- 2008-06-23: SCARNA_LM ver2.0
- SCARNA_LM ver2.0 has been released.
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
Usage
./scarna_lm [options] : sequence file in multi fasta format options:-min_len N
use N for minimum alignment length
-min_num N
use N for minimum alignment number
Experimental Datasets
The dataset used in the pairwise alignment experiment is downlodable here. The dataset used in the local multiple alignment experiment is downlodable here. The scripts for evaluating the accuracies of local multiple alignment is downlodable here.References
Yasuo Tabei and Kiyoshi Asai,
A local multiple alignment method for detection of non-coding RNA sequences,
submitted
Tu Minh Phuong, Chuong B. Do, Robert C. Edgar and Serafim Batzoglou,
Multiple alignment of protein sequences with repeats and rearrangements.
Nucleic Acids Research 2006 34(20), 5932-5942
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
Chuong B. Do, Samuel S. Gross, and Serafim Batzoglou,
CONTRAlign: Discriminative Training for Protein Sequence Alignment,
Proceedings of the Tenth Annual International Conference on Computational Molecular Biology, (RECOMB 2006), pp. 160–164
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) Yasuo Tabei, Koji Tsuda, Taishin Kin, and Kiyoshi Asai
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.
