#acl All:read
LOLA (LOgos Look Amazing) is a tool for generating sequence logos using Position Weight Matrix based protein profiles. LOLA allows you to generate custom sequence logos by setting parameters such as logo height, trim percentage, and residue colour scheme. You can then save logos in various formats including PDF, PNG, and JPEG.

LOLA is currently in beta-testing. Version 1.1-beta is now available for download. 

[[TableOfContents()]]

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== Downloads ==
=== Latest Release ===
''LOLA Version 1.2 Beta (2008 May 12)''[[BR]]
Build: attachment:LOLA-1.2-beta.tgz [[BR]]
Source: attachment:LOLA-1.2-beta-src.tgz

=== Earlier Releases ===
''LOLA Version 1.1 Beta (August 22, 2007)''[[BR]]
Build: attachment:LOLA-1.1-beta.tgz [[BR]]
Source: attachment:LOLA-1.1-beta-src.tgz
 
==== Release Notes ====
'''Version 1.2 beta:'''
 * Logo trees can be generated for all types of domains - not only terminal binding
 * New advanced options including amino acid coloring styles, amino acid grouping, and logo tree leaf ordering
 
'''Version 1.1 beta:'''
 * New ''Logo Tree'' feature - basic functionality for PDZ or other terminal binding motifs not requiring profile alignment

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== Installing and Running ==
'''Requirements:''' Java Runtime Environment (JRE) 1.5 or later is required to run LOLA. All other dependencies are included in the download.

 * Extract the TAR file. This will create a directory named "lola".
 * On Linux, open the command shell and run "lola.sh" from the "lola" directory.
 * On Windows, double click "lola.bat".
 * On Mac, double click lola-1.0-beta.jar

LOLA accepts one or more [wiki:Self:../BRAIN/PeptideFile peptide file] as shown in the example below. A peptide file describes a protein containing a specific domain, and provides known peptide ligands of this domain obtained by an experimental technique. You can open a single peptide file, or multiple peptide files grouped into a [wiki:Self:../BRAIN/PeptideFile#ProjectFiles project file].

Here's a view of LOLA after opening a PDZ domain project file:

attachment:lolaScreenShot.png
attachment:lolaScreenShotLogoTree.png

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== Future Developments ==

 * Generate a "logo tree" by hiearchically clustering logos [Initial PDZ (no alignment) use case completed in version 1.1]
 * Allow colours to be selected for individual amino-acids
 * Add support for nucleic acids
 * Additional visualization options (e.g. font, axis labels)

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== Contact ==

If you have any questions or feedback, please email Moyez Dharsee at mdharsee@infochromics.com.