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 1.0-beta is now available for download. 

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=== Latest Download ===

LOLA Version 1.0 Beta: [attachment:lola-1.0-beta.tar Download]

=== Requirements ===

Java Runtime Environment (JRE) 1.5 or later is required to run LOLA. All other dependencies are included in the download.

=== Installing and Running ===

 * 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

 * You can open a single peptide file, or a project file linked to multiple peptide files.

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

attachment:lolaScreenShot.png

=== Input Format ===
LOLA accepts the BRAIN peptide file format. A peptide file describes a protein containing a specific domain, and provides known peptide ligands of this domain obtained by an experimental technique. Here's a sample:
{{{
Gene Name       WWP2
Accession       Refseq:NP_008945 Entrez:11060
Organism        Homo Sapiens (Human)
NCBITaxonomyID  9606
Domain Number   4
Domain Type     WW
Interpro ID     IPR001202
Technique       Peptide Chip
Domain Sequence PALPPGWEMKYTSEGVRYFVDHNTRTTTFKDPRPG
Domain Range    444-478
Comment
PeptideName     Peptide CloneFrequency  QuantData       ExternalIdentifier
1       NRLDLPPYETFEDX  1
2       RWDRPPPYVAPPSX  1
3       XXGYTGPPRPPPYG  1
4       XXPHPQPPPYGHCV  1
5       XXNFPAPPPYPGES  1
6       MTPYRSPPPYVPPX  1
7       PGTAPPPYTVGPGY  1
8       YVQPAPPPYPGPMG  1
9       YVQAPPPPYPGPMG  1
10      YVQPPAPPYPGPMG  1
11      TCICPPDYMQVNXX  1
12      HSPPLPPYTPPTLX  1
13      SRGLPPPYDLTWVN  1
14      CGTYPPSYNLTFXX  1
15      DDCQPPAYTYNNXX  1
16      SDLQPPNYYEVMXX  1
17      GLMRPPAYCDAKXX  1
18      YTDAPPAYSELYXX  1
19      STFKPPAYEDVVXX  1
20      SRGMPSYEEAVMAX  1
21      ATSFPPSYESVTXX  1
22      APSAPPSYEETVXX  1
23      NCDPPPTYEEATXX  1
24      LPEPPPPYEFSCXX  1
25      EPENPPPYEEAMXX  1
}}}

==== Header Section ====

 '''Gene Name:''' An identifier that represents the gene or protein sequence. Not required to be unique.

 '''Accession:''' A space-separated list of database accession identifier for the protein or corresponding gene.

 '''Organism:''' Description of taxon of the protein.

 '''NCBITaxonomyID:''' Taxon identifier from NCBI's Taxonomy repository.

 '''Domain Number:''' A number that represents the position of the domain sequence within the protein. For proteins containing multiple instances of the domain, this number helps distinguish the position of these instances.

 '''Domain Type:''' The formal name of the domain, e.g. WW, PDZ, SH3.

 '''InterproID:''' The Interpro database identifier for the domain.

 '''Technique:''' The experimental method used to identify potential ligands of the protein.

 '''Domain Sequence:''' The amino-acid sequence of the domain region.

 '''Domain Range:''' The amino-acid position range for the domain region within the protein.

 '''Comment:''' Notes, additional information, personal comments pertaining to this file.

==== Peptide Section ====

 '''PeptideName:''' A ''unique'' incremental number assigned to each peptide ligand.

 '''Peptide:''' The peptide ligand sequence.

 '''CloneFrequency:''' Applies only to phage display data: the observed frequency of the peptide in the cloning step.

 '''QuantData:''' A number that relatively or absolutely quantifies the protein-ligand interaction. E.g. The optical density (OD) from a protein chip experiment.

 '''ExternalIdentifier:''' A database identifier for the peptide. E.g. from the DOMINO repository.


=== Future Developments ===

 * Generate a "logo tree" by hiearchically clustering logos
 * Allow colours to be selected for individual amino-acids
 * Add support for nucleic acids
 * Additional visualization options (e.g. font, axis labels)

=== Contact ===

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