<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;"> >sudo perl -MCPAN -e shell<br> >Password: ********<br> >install Storable<br> >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;"> > 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% Feedback on %BASEWEB%.%BASETOPIC%"}%
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SupplementRiboswitchPrediction_v1
Topic revision: r2 - 2007-12-20 - JeffreyBarrick