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| #acl All:read | |
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| LOLA is currently in beta-testing. Version 1.0-beta is now available for download. | LOLA is currently in beta-testing. Version 1.1-beta is now available for download. |
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| === Latest Download === | ---- == 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 |
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| LOLA Version 1.0 Beta: [attachment:lola-1.0-beta.tar Download] | === 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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| === 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 === |
---- == 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. |
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| * You can open a single peptide file, or a project file linked to multiple peptide files. | 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]. |
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| Here's a view of LOLA after opening a PDZ domain project file: | Here's a view of LOLA after opening a PDZ domain project file, and after generating a logo tree: |
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| attachment:lolaScreenShot.png | attachment:lolaScreenShot-Small.png attachment:lolaScreenShotLogoTree.png |
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| === 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. |
---- == Future Developments == |
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| 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 '''*'''. '''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. '''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. 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 |
* Generate a "logo tree" by hiearchically clustering logos [Initial PDZ (no alignment) use case completed in version 1.1] |
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| === Contact === | ---- == Contact == |
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.
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
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, and after generating a logo tree:
attachment:lolaScreenShot-Small.png attachment:lolaScreenShotLogoTree.png
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)
Contact
If you have any questions or feedback, please email Moyez Dharsee at mdharsee@infochromics.com.