ToolsRNAStructureMutualInformation < Lab

<table><tr><td width=88><img src="%PUBURL%/%WEB%/SharedImages/wip.gif"></td> <td valign="center"><b><font color="red" size=+2>Warning!</font><br><font size="+1">This page is under construction. The instructions are currently not complete!</font></b></td></tr></table>

---+ Mutual Information Support for RNA Secondary Structure Models

Predicting base interactions in RNA structures from the phylogenetic-significance of mutual information between columns.

%TOC%

---++ Overview: What do these programs do?

Reference.

---++ Install a modified version of rate4site

The program <b>[[http://www.tau.ac.il/~itaymay/cp/rate4site.html][rate4site]]</b> is used to infer a phylogenetic tree with per-site substitution rates that generates the observed sequence alignment. In order to properly function on RNA alignments, <b>rate4site</b> required a minor source code modification to deal with gap characters as a separate state. For convenience, I have included this modification on the latest source release for download here.

| [[%ATTACHURL%/rate4site.tgz][%ICON{download}% Download <b>rate4site</b>]] | version 2.01 (Nov06) modified | 18 December 2008 |

The included Makefile is for compiling under Windows. To compile use this command instead:

<code><div style="border-color: grey; border-style: solid; border-width: 1px; padding:1px;">
g++ -Dunix -DDOUBLEREP -o rate4site -O3 *.cpp
</div></code>

Finally, add the new <b>rate4site</b> executable to your $PATH so that the mutual information scripts can employ it.

---++ Install the esl-weight program from Infernal

Chances are that you already have Infernal installed if you routinely work with RNA alignments. If not, download Infernal, compile, and install according to the included instructions.

| [[http://infernal.janelia.org/][%ICON{external}% Official Infernal Site]] |

These scripts actually only need the <b>weight</b> or <b>esl-weight</b> utility program that is included. This program will be compiled, but may NOT be installed by default. For infernal-1.0rc5, you can find the binary at =infernal-1.0rc5/easel/miniapps/esl-weight=. Either move this into a =bin= directory or add it to your $PATH so that the mutual information scripts can employ it.

Attachments

Topic attachments
I	Attachment	History	Action	Size	Date	Who	Comment
tgz	rate4site.tgz	r1	manage	218.9 K	2008-12-18 - 20:39	JeffreyBarrick

This topic: Lab > ToolList > ToolsRNAStructureMutualInformation
Topic revision: r2 - 2008-12-18 - JeffreyBarrick