| 1 | 1.Program name |
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| 2 | MXSCARNA |
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| 3 | |
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| 4 | 2.Author |
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| 5 | Yasuo Tabei |
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| 6 | |
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| 7 | Department of Computational Biology, |
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| 8 | Graduate School of Frontier Science, |
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| 9 | The University of Tokyo |
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| 10 | and |
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| 11 | Computational Biology Research Center (CBRC), |
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| 12 | National Institute of Advanced Industrial Science and Technology (AIST) |
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| 13 | |
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| 14 | E-mail: scarna@m.aist.go.jp |
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| 15 | |
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| 16 | 3.What is MXSCARNA |
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| 17 | MXSCARNA (Multiplex Stem Candidate Aligner for RNAs) is a tool for |
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| 18 | fast structural multiple alignment of RNA sequences using progressive |
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| 19 | alignment based on pairwise structural alignment algorithm of SCARNA. |
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| 20 | |
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| 21 | 4.License |
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| 22 | While its original source code is provided as free software, MXSCARNA |
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| 23 | contains the source codes of ProbCons and Rfold and the energy parameters |
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| 24 | of Vienna RNA package (version 1.5). |
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| 25 | The author thanks Dr. Chuong Do, Dr. Hisanori Kiryu and Dr. Ivo Hofacker, |
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| 26 | the authors of ProbCons, Rfold and Vienna RNA package respectively, |
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| 27 | and Institute for Theoretical Chemistry of the University of Vienna. |
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| 28 | |
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| 29 | The source code of Rfold is located in ./src/rfold-0.1, which includes |
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| 30 | energy parameters of Vienna RNA package in ./src/rfold-0.1/src/vienna. |
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| 31 | Energy parameters of Vienna RNA package are also included in the source |
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| 32 | code of MXSCARNA (./src/vienna). Please follow ./src/rfold-0.1/readme.txt |
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| 33 | file, which describes the license of Rfold, and |
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| 34 | ./src/rfold-0.1/src/vienna/COPYING file and ./src/vienna/COPYING file, |
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| 35 | which describe the copyright notice of the Vienna RNA package. |
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| 36 | The source code of ProbCons is located in ./src/probconsRNA. Please follow |
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| 37 | ./src/probcons/README. |
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| 38 | |
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| 39 | The original part of MXSCARNA is provided as free software. It is |
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| 40 | distributed in the hope that it will be useful but WITHOUT ANY WARRANTY; |
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| 41 | without even the implied warranty of MERCHANTABILITY or FITNESS FOR A |
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| 42 | PARTICULAR PURPOSE. |
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| 43 | |
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| 44 | Permission is granted for research, educational, and commercial use |
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| 45 | and modification so long as |
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| 46 | 1) the package and any derived works are not redistributed for any fee, |
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| 47 | other than media costs, |
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| 48 | 2) proper credit is given to |
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| 49 | the authors of MXSCARNA, ProbCons, Rfold and Vienna RNA package, |
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| 50 | the Univeristy of Tokyo, |
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| 51 | Computational Biology Research Center (CBRC), AIST |
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| 52 | and Institute for Theoretical Chemistry of the University of Vienna. |
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| 53 | |
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| 54 | If you want to include this software in a commercial product, please |
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| 55 | contact the author. |
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| 56 | |
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| 57 | 5.Citation |
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| 58 | Yasuo Tabei, Hisanori Kiryu, Taishin Kin, Kiyoshi Asai: |
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| 59 | "A fast structural multiple alignment method for long RNA sequences," |
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| 60 | BMC bioinformatics, to appear. |
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| 61 | |
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| 62 | 6.References |
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| 63 | |
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| 64 | Do, C.B., Mahabhashyam, M.S.P., Brudno, M., and Batzoglou, S. 2005. |
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| 65 | PROBCONS: Probabilistic Consistency-based Multiple Sequence Alignment. |
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| 66 | Genome Research 15: 330-340. |
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| 67 | |
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| 68 | Hisanori Kiryu, Taishin Kin, and Kiyoshi Asai |
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| 69 | Rfold: An exact algorithm for computing local base pairing probabilities |
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| 70 | Bioinformatics, Advance Access published on December 4, 2007; |
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| 71 | doi:10.1093/bioinformatics/btm591 |
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| 72 | |
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| 73 | Ivo L. Hofacker |
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| 74 | Vienna RNA secondary structure server |
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| 75 | Nucleic Acids Res., Jul 2003; 31: 3429 - 3431. |
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| 76 | |
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| 77 | Yasuo Tabei, Koji Tsuda, Taishin Kin, and Kiyoshi Asai |
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| 78 | SCARNA: fast and accurate structural alignment of RNA sequences by matching fixed-length stem fragments |
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| 79 | Bioinformatics 2006 22(14):1723-1729. |
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| 80 | |
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| 81 | 7.Install |
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| 82 | The program was tested using gcc 3.3.3 on linux machines and gcc 3.4 on |
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| 83 | cygwin Some gcc specific features are currently used. |
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| 84 | |
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| 85 | The command to compile this software is as follows: |
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| 86 | |
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| 87 | make |
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| 88 | cd program |
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| 89 | |
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| 90 | 8.Usage |
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| 91 | |
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| 92 | ./mxscarna [options] seqfile |
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| 93 | |
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| 94 | seqfile: |
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| 95 | sequence file is multi fasta format. |
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| 96 | |
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| 97 | options: |
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| 98 | -clustalw |
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| 99 | use CLUSTALW output format instead of MFA |
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| 100 | |
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| 101 | -stockholm |
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| 102 | use STOCKHOLM output format instead of MFA |
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| 103 | |
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| 104 | -mxscarna |
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| 105 | use original output format instead of MFA |
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| 106 | |
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| 107 | -l <SCSLENGTH> |
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| 108 | the length of stem candidates (default:2) |
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| 109 | |
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| 110 | -b <BASEPROBTHRESHOLD> |
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| 111 | the threshold of base-pairing probability (default:0.01) |
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| 112 | |
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| 113 | -g <BASEPAIRSCORECONT> |
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| 114 | the control parameter of the prediction of base-pairs, (default:6) |
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| 115 | |
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| 116 | -rfold |
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| 117 | use Rfold instead of global McCaskill algorithm to calcurate base |
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| 118 | paring probality matrices, (default: off) |
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| 119 | |
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| 120 | -w <BANDWIDTH> |
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| 121 | the control parameter of the distance of stem candidates, (default:500) |
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| 122 | |
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| 123 | 9.Example |
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| 124 | ./mxscarna -mxscarna ../sample/trna.mfa |
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| 125 | |
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| 126 | 10.Version History |
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| 127 | 1. 1/16/2008 (Yasuo Tabei) |
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| 128 | -- MXSCARNA ver 2.0 release |
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| 129 | - Rfold was included. |
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