stoat

NAME
SYNOPSIS
DESCRIPTION
OPTIONS
ENVIRONMENT
EXAMPLES
REFERENCES
CITE
VERSION
LICENSE
AUTHORS

NAME

stoat − calculate statistical values of secondary structures

SYNOPSIS

stoat −i name_of_input_file [−o prefix_name_of_output_file] [−x number_of_character_states] [−h] [−v] [−f "RNAfold_arguments"] [−t] [−r]

DESCRIPTION

stoat calculates four statistical values from the secondary structure of folded RNA strings. The RNA strings are fed to the program through an input file in the FASTA format and the secondary structure of the various input sequences are obtained by interactions with the RNAfold program from the Vienna package. The four statistical values are the Shannon entropy, the Forbenius norm, the Base-pairing propensity and the mean stem length. The calculations are presented in two NEXUS formated files where each row in the matrix represents the statistical values of each input sequence.

stoat also translates the secondary structure (either provided by the user or obtained from RNAfold) from the bracket notation to the DCSE format. This translator only translate each sequence separately and does not do any type of alignment between the various sequences in the input file.

OPTIONS

The following options can be used with stoat. For a list of the RNAfold options, please see the RNAfold man page at http://www.tbi.univie.ac.at/~ivo/RNA/RNAfold.html

−i

The name of the FASTA formated input file. The input file typically contains more than one RNA sequence.

−o

The prefix name of the output file. The output file names ends with ’_l.nex’, ’_g.nex’ and ’.dcse’. The ’_l.nex’ file gives the character states relative to the min and max values of that run where as the ’_g.nex’ gives the character states relative to 0 and 1.

−x

Change the number of character states in the NEXUS files. Default is 31 and maximum is 64.

−h

Prints help to standard out.

−v

Gives verbose output to standard out.

−f

Arguments to be used by RNAfold. These parameters have to be enclosed in " ". The default arguments used with RNAfold are "-p -d2 -noLP".

−t

Use the constrained input structure and not the RNAfolded secondary structure to generate the DCSE format.

−r

Make a flipped character state matrix. Rows becomes columns and vice versa.

ENVIRONMENT

PATH

RNAfold needs to bee in $PATH.

EXAMPLES

The minimum number of arguments needed to run stoat:

stoat −i name_of_input_file

REFERENCES

The equations used to calculate the Shannon entropy, the Forbenius norm, the Base-pairing propensity and the mean stem length were found in the two following papers:

[1]

E. A. Schultes, P. T. Hrabrer and T. H. LaBean, Estimating the Contributions of Selection and Self-Organization in RNA Secondary structure, Journal of Molecular Evolution, Pages 76-83, 1999.

[2]

P. P. Gardner, B. R. Holland, V. Moulton, M. Hendy and D. Penny, Optimal Alphabets for an RNA World, The Royal Society of London B, Pages 1177-1182, 2003.

CITE

Please cite in the following manner if you choose to use stoat:

V. Knudsen and G.Caetano-Anolles, Some title of a paper published in some journal.

VERSION

This man page documents stoat version 0.1.

LICENSE

Copyright 1999-2007 by Vegeir Knudsen. All rights reserved.

Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met:

1.

Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.

2.

Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.

DISCLAIMER:

THIS SOFTWARE IS PROVIDED BY THE AUTHOR ‘‘AS IS’’ AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

AUTHORS

Vegeir Knudsen and Gustavo Caetano-Anolles.