Motif Distribution Viewer              Download    Help

Files (software packages of MDV) for download

You can use MDV in your computer !

This page provides the two programs. These programs are the products of Genome information integration project.
  1. Motif Distribution viewer (MDV) [Obsolete !! The new version is coming soon.]>. This web tool. You can download this program, and install and use MDV.
    Note: The MDV program uses the library of jfreechart1.1 (http://www.jfree.org/), which is provided under LGPL license (thanks to David Gilbert and Thomas Morgner). We arranged two Java files in the library. For the change-log, see here.

  2. Utility: JASPARtoMotifscanner.
    We provide a simple Java program with a shell script that can be used to input JASPAR matrix files (*.pfm) and a 'matrix_list.txt' and output a matrix file in a format suitable for MotifScanner.
  3. Test: JSTfile.

Local Use of Motif Distribution Viewer (MDV)

Requirements

Installation

  1. Prepare two datasets: Sequence and related files and motif files. You can get the sample dataset from here.
    1. Sequence and related files.
      Set one or multiple sequence files (FASTA files) in multi-FASTA format at an arbitrary directory (e.g. at /home/you/data/geneset.fa). Each FASTA file will be the items of the menu of Step 1 in the analysis.
    2. Motif positon file (optional)
      To view the distribution of motif instances using the matrix type motifs (PWMs), the motifs and their positions on the sequences must be predicted and converted to General Feature Format (GFF; http://www.sanger.ac.uk/Software/formats/GFF/). A typical tool employed for prediction using PWMs is MotifScanner, which outputs the prediction in GFF format. Use the second program "JASPARtoMotifScanner" shown above.
  2. Install JDK and Tomcat, and start Tomcat (on Linux, run tomcat/bin/startup.sh).
  3. Deploy the war file "DistributionViewer.war". (put war file to directory: apache-tomcat-5.5.x/webapps)
  4. Access to the URL http://localhost:8080/DistributionViewer. Then, Java will unzip and deploy this war file.

Configuration

  1. Edit the property file. The deploy path is (For example :"apache-tomcat-5.5.x/webapps/DistributionViewer/WEB-INF/classes/resources/System.properties").
  2. Set the variable alignmentDir as the directory where the prepared gff and FASTA file exist.

    3. #-----Path------
    #user data file name
    alignmentDir =/home/you/data
    MatchedPath =/home/you/data
    URI =http://localhost:8080/DistributionViewer

  3. If necessary, extend the heap memory of Tomcat. To do that, edit the file "apache-tomcat-5.5.x/bin/catalina.sh", and restart Tomcat. We show an example of the configuration files below for Tomcat 5.5.x on Linux. The option "-Xmx" is to set the size of the heap memory. When you are using the sample sequence files obtained above, you must extend JVM heap memory at least to 800MB in 32 bit OS.

    4. # JSSE_HOME (Optional) May point at your Java Secure Sockets Extension
    # (JSSE) installation, whose JAR files will be added to the
    # system class path used to start Tomcat.
    # # CATALINA_PID (Optional) Path of the file which should contains the pid
    # of catalina startup java process, when start (fork) is used
    # $Id: catalina.sh,v 1.16 2004/07/28 15:49:19 yoavs Exp $
    # -----------------------------------------------------------------------------
    # PARAM sample your setting -----------------------------------------------------------
    JAVA_HOME=/usr/java/java1.5
    PATH=$PATH:$JAVA_HOME/bin
    CLASSPATH=.:$JAVA_HOME/lib/tools.jar
    CATALINA_OPTS="-Xmx800M -Xms64M -Xss256k "
    export CATALINA_OPTS
    #--------------------------------------------------------------------------

  4. Restart Tomcat. Use "tomcat/bin/shutdown.sh" and "tomcat/bin/startup.sh" on Linux.
  5. Access http://localhost:8080/DistributionViewer and confirm it is running.