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| == LOLA == |
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| LOLA Version 1.0 Beta: attachment:lola-1.0-beta.tar | LOLA Version 1.0 Beta: [attachment:lola-1.0-beta.tar Download] |
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| * 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. 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. 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 ==== 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 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 ==== Describes the experimentally determined peptide ligands. 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. E.g. from the DOMINO repository. |
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.
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.
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.
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
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 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
Describes the experimentally determined peptide ligands. 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. 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.