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 1.36 is now available for download.


Downloads

Latest Release

LOLA Version 1.36 (April 4, 2012) Build (verified to run with jre 1.6.0_22): LOLA-1.36.zip

Current Development Release

LOLA Version 1.36 (April 4, 2012) Source + dependencies (verified to run with jre 1.6.0_22): LOLA-1.36-src.zip

Earlier Stable Releases

LOLA Version 1.35 Alpha (June 5, 2009)
Build: LOLA-1.35-alpha.zip (verified to run with jre 1.6.0_22)

LOLA Version 1.3 Beta (September 29, 2008)
Build: LOLA-1.3-beta.tgz
Source: LOLA-1.3-beta-src.tgz

LOLA Version 1.2 Beta (May 12, 2008)
Build: LOLA-1.2-beta.tgz
Source: LOLA-1.2-beta-src.tgz

LOLA Version 1.1 Beta (August 22, 2007)
Build: LOLA-1.1-beta.tgz
Source: LOLA-1.1-beta-src.tgz

Release Notes

Version 1.36:

Version 1.35 alpha:

Version 1.3 beta:

Version 1.2 beta:

Version 1.1 beta:


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.

LOLA accepts one or more peptide files 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 project file.

LOLA also accepts one or more pwm files as shown in the example below. A pwm file describes a position weight matrix (rows are amino acids, columns are ligand positions) where each cell in the matrix represents the frequency of observing a specific amino acid at a given ligand position. You can open a single pwm file, or multiple pwm files grouped into a project file.

Here's a view of LOLA after opening a PDZ domain project file, and after generating a logo tree:

lolaScreenShot-Small.png [ATTACH]

Changing memory allocations on Windows, Mac, and Linux machines

There are a number of ways to change LOLA's memory allocation, depending on your preferred method of opening the application.

Option A: Command line startup (note: this does not permanently change LOLA's default 512M setting)

If you are opening LOLA from the command-line using the command:

then you can increase the value of –Xmx to the desired amount of memory. For example:

Option B: Using lola.bat (Windows systems)

  1. Open the file lola.bat in a text editor (eg. right-click and select Open With Notepad).
  2. Increase the value of the –Xmx tag (found in the last line of the file), as per Option A. Do not modify other parts of the file.
  3. Save and close the file.
  4. Open LOLA by double-clicking on lola.bat.

Option C: Using lola.sh (UNIX, Linux, and Mac OS X systems)

  1. Open the file lola.sh in a text editor (eg. right-click and select Open With TextEdit).

  2. Increase the value of the –Xmx tag (found in the last line of the file), as per Option A. Do not modify other parts of the file.
  3. Save and close the file.
  4. Open LOLA by running lola.sh from the command-line.


References

LOLA has been referenced in the following publications:

Tonikian, R.

et al.(2008) A Specificity Map for the PDZ Domain Family.

PLOS Biology, 6, 9: 2043-2059.

http://biology.plosjournals.org/perlserv/?request=get-document&doi=10.1371/journal.pbio.0060239


Future Developments


Contact

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

Software/LOLA (last edited 2012-04-04 21:44:18 by ShirleyHui)

MoinMoin Appliance - Powered by TurnKey Linux