SupplementRiboswitchPrediction

<noautolink>
<div style="background-color:yellow;"> Note: _This supplement / protocol is still under construction._ </div>

---++ Predicting Riboswitch Regulation on a Genomic Scale

This page describes how to install a set of Perl scripts designed to identify members of known [[http://en.wikipedia.org/wiki/Riboswitch][riboswitch classes]] in genomic sequences. It accompanies a _[[http://www.humanapress.com/index.php?option=com_searchresult&task=favorites&search=Methods%20in%20Molecular%20Biology&category=books][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 [[http://www.sanger.ac.uk/Software/Rfam/][Rfam database]], or for investigating new regulatory RNA motifs, such as might be predicted by [[http://bio.cs.washington.edu/yzizhen/CMfinder/][CMfinder]].

---+++ Installation

---++++ Code Libraries

[[http://www.libgd.org/Main_Page][libGD]] is required to produce drawings of the the genomic contexts of putative RNA structure matches. Download and install according to the directions on your system.

---++++ Perl Modules

Several additional Perl modules from are required for the riboswitch perl scripts. You can download and install them directly from [[http://www.cpan.org/][CPAN]]. Alternately, on MacOS X, you can use the following command sequence:

<code><div style="border-color: grey; border-style: solid; border-width: 1px; padding:1px;">
&nbsp;&gt;sudo perl -MCPAN -e shell<br>
&nbsp;&gt;Password: ********<br>
&nbsp;&gt;install Storable<br>
&nbsp;&gt;install GD<br>
</div></code>

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 <code>module.pm</code> in @INC", try installing <code>module</code> from CPAN.

---++++ <nop>BioPerl

As of December 2007, neither the stable or development releases of <nop>BioPerl (1.4.0 or 1.5.2) includes the necessary modules for parsing Infernal search results or manipulating Stockholm alignments. Therefore, you will need to download and install the current CVS version of *bioperl-live*. Either follow the [[http://www.bioperl.org/wiki/Getting_BioPerl][Getting BioPerl]] instructions or try this link to [[http://code.open-bio.org/cgi/viewcvs.cgi/bioperl-live/bioperl-live.tar.gz?tarball=1][download directly]].

---++++ Riboswitch Perl Scripts

Download the riboswitch Perl scripts.

| [[bob][%ICON{download}%]] | version 1.0 | December 2007 |

---+++ Usage

Each Perl script has POD documentation. Either open the script a text editor to view it or use the <code>perldoc</code> command:
<code><div style="border-color: grey; border-style: solid; border-width: 1px; padding:1px;">&nbsp;&gt; perldoc genome_context.pl</div></code>

Questions, comments, or problems with this procedure? %MAKETEXT{"<a href='[_2]'>Send feedback</a>" args="<nop>%WIKITOOLNAME%,mailto:%WIKIWEBMASTER%?subject=%WIKITOOLNAME%&#32;Feedback&#32;on&#32;%BASEWEB%.%BASETOPIC%"}%
This topic: Lab > SupplementList > SupplementRiboswitchPrediction_v1
Topic revision: r2 - 2007-12-20 - JeffreyBarrick