|
Size: 5131
Comment:
|
Size: 6954
Comment:
|
| Deletions are marked like this. | Additions are marked like this. |
| Line 20: | Line 20: |
| The BRAIN library and plugin are available below for download as Java archive (JAR) files and Java source tree tarballs. | |
| Line 21: | Line 22: |
| === Latest Build Release === | === Latest Release === |
| Line 23: | Line 24: |
| ''BRAIN Plugin'': Version 1.0.5 alpha (2007 May 23) [[BR]] | ''BRAIN Plugin'': Version 1.0.5 alpha (May 23, 2007) [[BR]] |
| Line 27: | Line 28: |
| ''BRAIN Library'': Version 1.0.6 (2007 July 26) [[BR]] Build: attachment:brainlib-1.1.jar [[BR]] Source: attachment:BRAIN-Library-1.2-src.tgz |
''BRAIN Library'': Version 1.4 (September 29, 2008) [[BR]] Build: attachment:brainlib-1.4.jar [[BR]] Source: To be posted by October 3, 2008 |
| Line 32: | Line 33: |
=== Earlier Releases === ''BRAIN Library'': Version 1.3 (May 12, 2008) [[BR]] Build: attachment:brainlib-1.3.jar [[BR]] Source: attachment:BRAIN-Library-1.3-src.tgz |
|
| Line 38: | Line 45: |
| * Java Runtime Environment (JRE) 1.5 or later is required to run BRAIN Plugin. | * Java Runtime Environment (JRE) 1.5 or later |
| Line 53: | Line 60: |
| BRAIN takes one or more query proteins and their respective peptide ligands, builds a PSSM-based profile for each protein, searches a protein sequence database for similar profiles, and returns a ranked set of proteins that are predicted to interact with the query proteins. | BRAIN takes one or more query proteins and their respective peptide ligands, builds a PWM-based profile for each protein, searches a protein sequence database for similar profiles, and returns a ranked set of proteins that are predicted to interact with the query proteins. |
| Line 55: | Line 62: |
| A query protein along and its experimentally determined peptide ligands are represented as a [wiki:/PeptideFile peptide file]. The plugin can open a single peptide file, or multiple peptide files that are grouped into a [wiki:/PeptideFile#Project Files:Link project file]. | A query protein and its experimentally determined peptide ligands are represented as a [wiki:/PeptideFile peptide file], in which the peptide binders are listed as an ungapped multiple sequence alignment. The plugin can open a single peptide file, or multiple peptide files that are grouped into a [wiki:/PeptideFile#ProjectFiles project file]. From a peptide file, BRAIN generates a position weight matrix (PWM), or protein profile. The profile constitutes the distributions of amino acids (rows) at each of the positions (columns) of the peptide pattern. In a given column of the PWM, each amino acid is assigned a weight based on its frequency of occurrence at the given position. These weights are normalized to 1.0 to emulate probabilities of occurrence. BRAIN searches a protein sequence database (in FASTA, Swiss``Prot, Gen``Pept, or EMBL format) for the pattern represented by the protein profile. An interaction score (p-value) is calculated for each hit, and all hits exceeding the user-provided score threshold are reported as predicted interactors of the query protein. The output is provided as a Cytoscape network, enabling further graph-based analysis and exploration of node (protein) and edge (interaction) attributes including interaction score, gene name, motif sequence, and associated OMIM or Morbid``Map record (if available). |
| Line 59: | Line 68: |
| '''BRAIN Library 1.1''' (2007 July 26) | '''BRAIN Library 1.4''' (September 29, 2008) * Supports the Cytoscape Task API to display a progress bar during logo tree generation '''BRAIN Library 1.3''' (May 12, 2008) * Single linkage hierarchical clustering used to cluster profiles for generating logo tree * Sequence logo alignment algorithm added for generating logo trees * New code for amino acid grouping and coloring schemes to be defined, e.g. for generating sequence logos and logo trees '''BRAIN Library 1.2''' (February 2008) * Internal release for alpha-testing '''BRAIN Library 1.1''' (July 26, 2007) |
| Line 62: | Line 82: |
| '''1.0.6''' (2007 June 12) * brain.jar: Ability to retrieve additional database references from ProteinProfile object (previously was only able to retrieve the first ID in the Accession field of the peptide file). |
'''1.0.6''' (June 12, 2007) * brain.jar: Ability to retrieve additional database references from Protein``Profile object (previously was only able to retrieve the first ID in the Accession field of the peptide file). |
| Line 65: | Line 85: |
| '''1.0.5''' (2007 May 23) | '''1.0.5''' (May 23, 2007) |
| Line 68: | Line 88: |
| '''1.0.4''' (2007 May 15) | '''1.0.4''' (May 15, 2007) |
| Line 73: | Line 93: |
| '''1.0.3''' (2007 April 23) | '''1.0.3''' (April 23, 2007) |
| Line 77: | Line 97: |
| '''1.0.2''' (2007 April 11) | '''1.0.2''' (April 11, 2007) |
| Line 82: | Line 102: |
| '''1.0.1''' (2007 February 21) | '''1.0.1''' (February 21, 2007) |
| Line 90: | Line 110: |
| Line 92: | Line 111: |
| Line 94: | Line 112: |
| Line 96: | Line 113: |
1. New feature: consider aa groups in correlation matrix |
BRAIN Project
The Biologically Relevant Analysis of Interaction Networks (BRAIN) is a set of algorithms for predicting and analyzing protein domain-peptide ligand interactions based on experimentally known binding evidence (e.g. from protein chip or phage display experiments).
BRAIN can be accessed as a Cytoscape plugin which reads peptide binding profiles and generates interactions displayed as a Cytoscape network.
BRAIN consists of a library or API, and of a Cytoscape plugin.
BRAIN Library
The BRAIN library holds the algorithms and methods for interaction prediction. This library is required to build the BRAIN plugin.
BRAIN Plugin
The BRAIN plugin is a way of running various BRAIN algorithms from the Cytoscape user interface. The plugin runs a prediction analysis and presents the results visually as an interactive Cytoscape network.
Downloads
The BRAIN library and plugin are available below for download as Java archive (JAR) files and Java source tree tarballs.
Latest Release
BRAIN Plugin: Version 1.0.5 alpha (May 23, 2007) BR Build: attachment:brainPlugin.jar BR Source: attachment:BRAIN-Plugin-1.0.5-src.tgz
BRAIN Library: Version 1.4 (September 29, 2008) BR Build: attachment:brainlib-1.4.jar BR Source: To be posted by October 3, 2008
Dependencies: Additional JARs required by BRAIN - attachment:brainDeps.tar.gz
Earlier Releases
BRAIN Library: Version 1.3 (May 12, 2008) BR Build: attachment:brainlib-1.3.jar BR Source: attachment:BRAIN-Library-1.3-src.tgz
Installing the Plugin
System Requirements
- Java Runtime Environment (JRE) 1.5 or later
[http://www.cytoscape.org Cytoscape] 2.4.1 or later
Installation
Place brainPlugin.jar and brainlib_1.1.jar in the Cytoscape plugins directory (located in the Cytoscape program directory, e.g. /usr/local/bin/Cytoscape or C:\Program Files\Cytoscape_v2.4.1)
Extract and place all files from brainDeps.tar.gz into the Cytoscape lib directory (located in the Cytoscape program directory)
- Launch Cytoscape
Look in the Plugins menu for the BRAIN item. If you don't see it there, revisit the above steps to make sure all files are in the right place.
Running the Plugin
- Launch Cytoscape
Set analysis parameters from Plugins > BRAIN > Set Parameters
Start the BRAIN analysis from Plugins > BRAIN > Run BRAIN
Notes on Using BRAIN
BRAIN takes one or more query proteins and their respective peptide ligands, builds a PWM-based profile for each protein, searches a protein sequence database for similar profiles, and returns a ranked set of proteins that are predicted to interact with the query proteins.
A query protein and its experimentally determined peptide ligands are represented as a [wiki:/PeptideFile peptide file], in which the peptide binders are listed as an ungapped multiple sequence alignment. The plugin can open a single peptide file, or multiple peptide files that are grouped into a [wiki:/PeptideFile#ProjectFiles project file]. From a peptide file, BRAIN generates a position weight matrix (PWM), or protein profile. The profile constitutes the distributions of amino acids (rows) at each of the positions (columns) of the peptide pattern. In a given column of the PWM, each amino acid is assigned a weight based on its frequency of occurrence at the given position. These weights are normalized to 1.0 to emulate probabilities of occurrence.
BRAIN searches a protein sequence database (in FASTA, SwissProt, GenPept, or EMBL format) for the pattern represented by the protein profile. An interaction score (p-value) is calculated for each hit, and all hits exceeding the user-provided score threshold are reported as predicted interactors of the query protein. The output is provided as a Cytoscape network, enabling further graph-based analysis and exploration of node (protein) and edge (interaction) attributes including interaction score, gene name, motif sequence, and associated OMIM or MorbidMap record (if available).
Release Notes
BRAIN Library 1.4 (September 29, 2008)
- Supports the Cytoscape Task API to display a progress bar during logo tree generation
BRAIN Library 1.3 (May 12, 2008)
- Single linkage hierarchical clustering used to cluster profiles for generating logo tree
- Sequence logo alignment algorithm added for generating logo trees
- New code for amino acid grouping and coloring schemes to be defined, e.g. for generating sequence logos and logo trees
BRAIN Library 1.2 (February 2008)
- Internal release for alpha-testing
BRAIN Library 1.1 (July 26, 2007)
- Added PDZ symbol style for PDZ type residue colouring in sequence logo generation code (required by LoLA tool)
1.0.6 (June 12, 2007)
brain.jar: Ability to retrieve additional database references from ProteinProfile object (previously was only able to retrieve the first ID in the Accession field of the peptide file).
1.0.5 (May 23, 2007)
- Code reorganization: brainPlugin.jar now holds only those classes related to the Cytoscape plugin. All other code has been moved to a new Brain Library project.
1.0.4 (May 15, 2007)
- Network node can represent a single domain or a protein containing multiple domain instances (via new Advanced Options tab)
- Lower scoring motif hits are now reported
New node attribute Domain Name to hold a semantic domain identifier (Gene Name + Domain Number, for now)
1.0.3 (April 23, 2007)
- Support for new peptide file format version 1.1 (and back-compatible with format version 1.0)
New node attributes Sequence Start, Sequence Stop, Comment for profiles generated from new peptide file format
1.0.2 (April 11, 2007)
- Report SNPs for entire protein sequence and for domain subsequence only.
- Option to specify codon bias file
- Option to load unique peptides only from peptide file(s)
1.0.1 (February 21, 2007)
- Port to Cytoscape API 2.4 and Java SE 5.0
Future Developments
(in order of priority)
- Regular expression filtering of profile search results.
- Expose auto-score threshold functionality in Profile Search panel (allow the user to specify automatic score threshold setting instead of having to specify a score threshold themselves).
- Expose "regex" search features - new Pattern Search panel similar to Profile Search
- New feature: consider aa groups in PWM searching
- Design an improved scoring scheme (e.g. take into account surface accessibility) and drop down box to select different scores.
Contact
If you have any questions or feedback, please email Moyez Dharsee at mdharsee@infochromics.com.