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 one or more 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.

The peptide file consists of a Header Section that describes the protein and domain sequence, and a Peptide Section that lists and describes the peptide ligands.

Example:

Gene Name       DLG1
Accession       Refseq:NP_004078
Organism        Homo Sapiens (Human)
NCBITaxonomyID  9606
Domain Number   3
Domain Type     PDZ
Interpro ID     IPR001478
Technique       Phage Display High Valency
Domain sequence KVVLHRGSTGLGFNIVGGEDGEGIFISFILAGGPADLSGELRKGDRIISVNSVDLRAASHEQAAAALKNAGQAVTIVA
Domain Range    466-525
Comment
PeptideName     Peptide CloneFrequency  QuantData       ExternalIdentifier
1       XLHFWRESSV      66
2       XXRLWKQTSL      3
3       ILKIWRETSL      3
4       KRTIWRETSL      2
A       KNLRSNSMLG      2
6       HLKFWRSTRV      2
7       AHSKWRSTSV      2
8       XXXHRRETTV      1
9       VISRWRQTSL      1
10      TTWLGRQTRV      1
11      SRSSYRETSV      1
12      XXXSRRETSV      1
13      RLFRYRETSL      1
B       PIRKRWTMTL      1
15      XXXNHRETSV      1
16      KIVRWKNTSV      1
17      KHRTWYETSV      1
18      XXXXFKQTSV      1
19      ARPKWRTTRV      1
20      ALPRRRETSV      1

Header Section

Describes the protein, domain, and experiment. Required fields are indicated with a *.

NOTE: This section is in a 2 column format. Field names must be separated from their values with a single TAB character. Multiple TABs or spaces are not accepted.

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

  Accession:* A space-separated list of database accession identifiers 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. Set to "0" if instance information is not known.

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

  Interpro ID: 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

Describes the experimentally determined peptide ligands. The peptide sequences must be in multiple alignment format. The sequences should contain no gaps, and should be padded with the X symbol on both sides, where required, such that all sequences have identical length.

NOTE: This section is in a 5-column format. Column headers and values must be separated with a single TAB character. Multiple TABs or spaces are not accepted.

Required fields are indicated with a *.

• PeptideName:* A unique numerical symbol assigned to each peptide ligand. To omit a peptide, set to a non-numeric value (e.g. "A"). Values in this column must be unique.

  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.

Using Project Files

To open several peptide files at once, simply link them all in a single project file. A project file is a text file containing the absolute paths of multiple peptide files. Opening the project file in LOLA will open each of the underlying peptide files in a single step, allowing logos to be constructed for multiple profiles.

Example:

#ProjectFile
/Users/moyez/research/ppi/profiles/PDZ/Human/SidhuPhage/APBA3-1.pep.txt
/Users/moyez/research/ppi/profiles/PDZ/Human/SidhuPhage/CASK-1.pep.txt
/Users/moyez/research/ppi/profiles/PDZ/Human/SidhuPhage/DLG1-1.pep.txt
/Users/moyez/research/ppi/profiles/PDZ/Human/SidhuPhage/DLG1-2.pep.txt
/Users/moyez/research/ppi/profiles/PDZ/Human/SidhuPhage/DLG1-3.pep.txt
/Users/moyez/research/ppi/profiles/PDZ/Human/SidhuPhage/DLG2-3.pep.txt
/Users/moyez/research/ppi/profiles/PDZ/Human/SidhuPhage/DLG3-2.pep.txt
/Users/moyez/research/ppi/profiles/PDZ/Human/SidhuPhage/DLG4-3.pep.txt
/Users/moyez/research/ppi/profiles/PDZ/Human/SidhuPhage/DVL2-1.pep.txt
/Users/moyez/research/ppi/profiles/PDZ/Human/SidhuPhage/ERBB2IP-1-hi.pep.txt

NOTE: The first line of the project file must contain the text "#ProjectFile".

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.