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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 1.2-beta is now available for download. |
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| === Latest Download === | ---- == Downloads == === Latest Release === ''LOLA Version 1.3 Beta (September 29, 2008)''[[BR]] Build: attachment:LOLA-1.3-beta.tgz [[BR]] Source: To be posted by October 2, 2008 |
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| LOLA Version 1.0 Beta: [attachment:lola-1.0-beta.tar Download] | === Earlier Releases === ''LOLA Version 1.2 Beta (May 12, 2008)''[[BR]] Build: attachment:LOLA-1.2-beta.tgz [[BR]] Source: attachment:LOLA-1.2-beta-src.tgz |
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| === Requirements === | ''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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| 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 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. |
=== Changing memory allocations on Windows, Mac, and Linux machines === |
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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. | There are a number of ways to change LOLA's memory allocation, depending on your preferred method of opening the application. |
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| 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 }}} |
==== Option A: Command line startup (note: this does not permanently change LOLA's default 512M setting) ==== |
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| ==== Header Section ==== | If you are opening LOLA from the command-line using the command: |
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| Describes the protein, domain, and experiment. Required fields are indicated with a '''*'''. | * java –Xmx512M –jar lola-VERSION.jar |
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| '''Gene Name:*''' An identifier that represents the gene or protein sequence. Not required to be unique. | then you can increase the value of –Xmx to the desired amount of memory. For example: |
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| '''Accession:*''' A space-separated list of database accession identifiers for the protein or corresponding gene. | * java –Xmx800M –jar lola-VERSION.jar |
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| '''Organism:''' Description of taxon of the protein. | ==== Option B: Using lola.bat (Windows systems) ==== |
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| '''NCBITaxonomyID:''' Taxon identifier from NCBI's Taxonomy repository. | 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. |
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| '''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. | ==== Option C: Using lola.sh (UNIX, Linux, and Mac OS X systems) ==== |
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| '''Domain Type:*''' The formal name of the domain, e.g. WW, PDZ, SH3. | 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. |
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| '''Interpro ID:''' The Interpro database identifier for the domain. | ---- == Future Developments == |
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| '''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 |
* Enable logo and logo tree parameters to be saved in a project file for later use * Support customized amino acid grouping schemes |
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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 1.2-beta is now available for download.
Downloads
Latest Release
LOLA Version 1.3 Beta (September 29, 2008)BR Build: attachment:LOLA-1.3-beta.tgz BR Source: To be posted by October 2, 2008
Earlier Releases
LOLA Version 1.2 Beta (May 12, 2008)BR Build: attachment:LOLA-1.2-beta.tgz BR Source: attachment:LOLA-1.2-beta-src.tgz
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
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:
- java –Xmx512M –jar lola-VERSION.jar
then you can increase the value of –Xmx to the desired amount of memory. For example:
- java –Xmx800M –jar lola-VERSION.jar
Option B: Using lola.bat (Windows systems)
- Open the file lola.bat in a text editor (eg. right-click and select Open With Notepad).
- 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.
- Save and close the file.
- Open LOLA by double-clicking on lola.bat.
Option C: Using lola.sh (UNIX, Linux, and Mac OS X systems)
Open the file lola.sh in a text editor (eg. right-click and select Open With TextEdit).
- 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.
- Save and close the file.
- Open LOLA by running lola.sh from the command-line.
Future Developments
- Enable logo and logo tree parameters to be saved in a project file for later use
- Support customized amino acid grouping schemes
- 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.