Predicting Riboswitch Regulation on a Genomic Scale

This page describes how to install a set of Perl scripts designed to identify members of known riboswitch classes in genomic sequences. It accompanies a Methods in Molecular Biology protocol chapter that explains how to use these scripts. This protocol may also be useful for analyzing other structured RNAs, such as those found in the Rfam database, or for investigating new regulatory RNA motifs, such as might be predicted by CMfinder.

Installation

Code Libraries

libGD is required to produce drawings of the genomic contexts of putative RNA structure matches. Download and install according to the directions for your system.

Perl Modules

Several additional Perl modules from are required for the riboswitch perl scripts. You can download and install them directly from CPAN. Alternately, on MacOS X, you can use the following command sequence if you have administrator privileges:

 >sudo perl -MCPAN -e shell
 >Password: ********
 >install Storable
 >install GD

The GD module requires libGD to be installed and is only necessary for producing genomic context drawings. If you encounter any other messages of the form: "Can't locate module.pm in @INC", try installing module from CPAN.

BioPerl

As of December 2007, neither the stable nor development releases of BioPerl (1.4.0 or 1.5.2) includes the necessary modules for parsing Infernal search results or manipulating Stockholm alignments. Therefore, you may need to download and install the current CVS version of bioperl-live. Either follow the Getting BioPerl instructions or try this link to download directly.

Riboswitch Perl Scripts

Download the riboswitch Perl scripts.

download version 1 6 January 2008

Usage

Each Perl script has POD documentation. Either open the script a text editor to view it or use one of these commands:

 > perldoc genome_context.pl
 > genome_context.pl --man

Questions, comments, or problems with this procedure? Send feedback

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Topic revision: r6 - 26 Aug 2008 - 02:04:49 - Main.JeffreyBarrick
 
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