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

6. 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 [email protected]