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资源说明：RNAFeatures: C library providing functions to compute several measures of RNA features including: measures for co-transcriptional folding effect and a measure for structural influences on selection in RNA genes.
RNAFeatures 1.0 ================================== Content ======= 0. Terms of use 1. Introduction 2. Theory 3. Usage 3.1. Installation 3.2. Invocation 3.3. Output 4. Citing RNAFeatures 5. Contact 0. Terms of use =============== Please read the file COPYING for licence terms. 1. Introduction =============== RNAFeatures computes two measures of RNA features: - co-transcriptional effect measures: Cis and Trans. - gene selection measures: class of bases and rate of substitution for each class. 2. Theory ========= The establishment of this theory is not my work. If you are interested in the theory, please read following papers: "Co-transcriptional folding is encoded within RNA genes" (http://www.biomedcentral.com/1471-2199/5/10/) written by Irmtraud M Meyer and Istvan Miklos. "An Analysis of Structural Influences on Selection in RNA Genes" (http://mbe.oxfordjournals.org/content/26/1/209.full.pdf) written by Naila K. Mimouni, Rune B. Lyngso, Sam Griffiths-Jones and Jotun Hein. "Moments of the Boltzmann distribution for RNA secondary structures" (http://ramet.elte.hu/~miklosi/MiklosMeyerNagy.pdf) written by Istvan Miklos, Irmtraud M. Meyer and Borbala Nagy. 3. Usage ======== This package includes both a library and executable program to compute above features of RNA sequences. 3.1. Installation ================= Please read INSTALL for details. 3.2. Invocation =============== RNAFeatures [options] [filename] RNAFeatures takes a file name, which containing a RNA sequence, as an input. Available command line options can be checked by following command: RNAFeatures -h You can test RNAFeatures on one of the example RNA sequences in a directory called "examples": e.g. RNAFeatures example/tRNA_seq e.g. RNAFeatures -g example/tRNA_seq 3.3. Output =========== RNAFeatures outputs following: - length of sequence - base pairs and closing loop - sequence - parenthesis structure - MFE - Cis and Trans - classes of each bases - The expected energy of the RNA secondary structure - The variance of the energy of the RNA secondary structure - MFE log probability of the RNA sequence 4. Citing RNAFeatures ===================== If you use RNAFeatures in your work, please cite: Irmtraud M Meyer and Istvan Miklos Co-transcriptional folding is encoded withing RNA genes. BMC Molecular Biology. 2004. 5:10 Naila K. Mimouni, Rune B. Lyngso, Sam Griffiths-Jones and Jotun Hein An Analysis of Structural Influences on Selection in RNA Genes Mol. Bio. Evo. 2009. 26:209-216 Istvan Miklos, Irmtraud M. Meyer and Borbala Nagy Moments of the Boltzmann distribution for RNA secondary structures Bull. Math. Biol. 2005. 67:1031-1047 5. Contact ========== Please feel free to contact the author for bug-reports, feature-requests, suggestions and etc. Of course I also look forward to hearing from you if you discovered something biologically interesting things using coTransFold. Katsuya Noguchi
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