<noautolink> ---+ 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.springer.com/humana+press/biochemistry/book/978-1-934115-88-6][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]]. <div style="background-color:rgb(255,200,200);margin:10px; padding:10px;"><table><tr><td width=88><img src="%PUBURL%/%WEB%/SharedImages/wip.gif"></td> <td valign="center"> *Please note:* Infernal and BioPerl have changed since this protocol was published, so the directions here differ somewhat from those in the book chapter. They are currently being updated. %MAKETEXT{"If you have any feedback, please contact [_1]" args="%WIKIWEBMASTER%"}%. See the [[SupplementRiboswitchPrediction_v1][original installation instructions (v1)]]. </td></tr></table></div> ---++ Installation ---+++ Code Libraries [[http://www.libgd.org/Main_Page][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 [[http://www.cpan.org/][CPAN]]. Alternately, on MacOS X, you can use the following command sequence if you have administrator privileges: <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 nor 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 may 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. | [[%ATTACHURL%/riboswitch_methods_v1.tar.gz][%ICON{download}%]] | version 1 | 6 January 2008 | ---++ Usage Each Perl script has POD documentation. To view it, either open the script in a text editor or use one of these commands: <code><div style="border-color: grey; border-style: solid; border-width: 1px; padding:1px;"> > perldoc genome_context.pl<br> > genome_context.pl --man</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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Topic revision: r1 - 2009-06-20 - JeffreyBarrick