marten

NAME
SYNOPSIS
DESCRIPTION
OPTIONS
EXAMPLES
CITE
VERSION
LICENSE
AUTHORS

NAME

marten − count the number of unpaired, paired and bulged nucleotides in folded RNA sequences

SYNOPSIS

marten −i name_of_input_file [−o prefix_name_of_output_file] [−S number_of_character_states] [−x the_size_of_the_search_space] [−h] [−v] [−e] [−r] [−s] [−p] [−a] [−m] [−n] [−g] [−V] [−P] [−l] [−R]

DESCRIPTION

marten counts the number of unpaired, paired and bulged nucleotides for each helix strand in the secondary structure of folded RNA sequences. The RNA sequences are fed into the program through an input file in the DCSE alignment format. The output of marten are presented (depending on the options used) as a NEXUS formated file and a text file referred to as the MARTEN file. In the character state matrix of the NEXUS formated file, each row represents one input sequence and each helix strand of the various input sequences is represented by three numbers. (These three numbers are the number of unpaired, paired and bulged nucleotides for that helix strand.) If the ’-P’ option is used, then the MARTEN file will display the various helix strands as ’x[y{z}]’. The characters ’x’, ’y’ and ’z’ are the number of unpaired, paired and bulged nucleotides respectively.

marten also translates the secondary structure of folded RNA sequences from the DCSE alignment format to the bracket notation. All the alignment information between the input sequences are lost during this translation.

OPTIONS

The following options can be used with marten.

−i

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

−o

The prefix name of the output file. The output file names ends with ’.mar’, ’.nex’, ’.fas’ and ’.con’. The ’.mar’ and ’.nex’ files are the MARTEN file and the NEXUS formated file respectively. Both the ’.fas’ and ’.con’ file are the output of the translator (DCSE -> bracket notation). In the ’.con’ file, the unpaired nucleotides are printed as ’x’ and the ’.con’ file can therefore be used as an input file to RNAfold to constrain the folding.

−S

Change the number of character states in the NEXUS files. Default is 64, which is also the maximum.

−h

Print a short help text to standard out.

−V

Print the version number.

−v

Give verbose output to standard out.

−r

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

−x

Change the number of positions outside the helix strands (’[]’) where marten looks for a helix number. Default is 0.

−e

Eliminate gaps (’-’) within the helix strands (’[]’).

−s

Summerize the number of nucleotides in each bulge (’{}’). (This option automatically includes the −e option.)

−p

Remove the non-standard pairing information (’()’).

−a

Summerize the number of nucleotides in all the bulges (’{}’) for each stem strand. (This option automatically includes the −s option.)

−m

Summerize the number of bases outside the stem strands (unpaired).

−n

Summerize the number of paired nucleotides in each helix strand. (This option automatically includes the −p option.)

−g

Remove the gaps (’-’) outside of the helix strands (’[]’).

−P

Make the NEXUS formated file with the character state matrix. (This option automatically includes the −e, −s, −p, −a, −m, −n and −g option. This option also activates the translator.)

−l

List the minimum and maximum values for each colum in the character state matrix.

−R

Add complementary numbers (unpaired, paired and bulged) for each helix and present the result in a separate character state matrix.

EXAMPLES

The minimum number of arguments needed to make the NEXUS file:

marten −i name_of_input_file −P

CITE

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

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

VERSION

This man page documents marten 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.