Genome Map Viewer (GMV) Tool

John Innes Centre, Norwich Research Park,
Colney Lane, Norwich, NR4 7UH, UK.

Telephone: +44(0) 1603 450597 (direct)
+44(0) 1603 450000 (switchboard)
Fax: +44(0)1603 450595

Introduction- Users Guide

The Genome Map Viewer is a tool that compares gene order in two or more genomes and displays the results in the form of the concentric ring display of Moore et al.(1995) and Gale and Devos (1998). This display shows the relative positions of linkage blocks in a set of species, where these blocks have been proposed on the basis of conservation of gene order across the species being examined. In cereals these blocks are often based on rice. Blocks are ordered within linkage groups (called chromosome blocks in GMV since they often represent a chromosom form a complete genome (called genome blocks within GMV for consistency) for the particular species.

Requirements

The software and hardware requirements for the running GMV tool are as follows.

When run as an applet for this site

1. A Java version 1.1 compatible browser.

When run as an application on your local machine.

1. A Java version 1.1 compatible interpreter. We recommend you install Sun's Java^TM 2 Runtime Environment (JRE) since with this version there is no need to install the archive (.jar) file before executing the application. If you are using MS windows NT/98 you need only double click on the archive file. If you are using UNIX then use the -jar flag, for example type at the command line the following

   Java -jar GMVTool.jar

2. The GMV Tool archive (GMVTool.jar) which is available in the GMVTool distribution in [.zip] or [.tar.gz] format. For your convenience all of the Java classes associated with CORBA interface to ACEDB (CITA)have been included in the GMVTool.jar file.
3. A CORBA ORB that supports the Java language mapping. Any Java CORBA ORB should do. If you have installed Java^TMJRE the GMV tool will automatically use the ORB included with the Java^TMJRE.

In addition to these requirements GMV tool needs access to a comparative database to perform comparative genome queries. In its default form the GMV tool uses the CORBA interface to ACEDB (CITA) to provide the data for these queries from the comparative database ComapDB. However, the GMV tool easily configured to access any ACEDB provided it follows the models for comparative data outlined in ComapDB. The GMV tool is designed to be able integrate with other database provided the linkage blocks data is consistent with the ComapDB models. However, additional Java code would be required, please look at our Developers page for further details.

Installation

If you wish run the application version of GMVTool or you wish the applet version to use the Java class on your local machine, and you are not using Sun's Java^TM 2 Runtime Environment (JRE) then you need to install the GMV Tool. You do this by decompressing the GMVTool_dist file you downloaded and then placing the GMV Tool archive (GMVTool.jar), contained within the distribution, in your computer's classpath. On the MS Windows NT/95/98 platform open the System control panel and click on the environment tag. Next add the path of the GMVTool.jar to the value held in the CLASSPATH variable. Each path in the value is separative by a semi-colon. So just add an addition semi-colon followed by the full path and file name of the GMVTool.jar. For example if GMVTool.jar is located in the directory E:\GMVTool\GMVTool.jar then add

;E:\GMVTool\GMVTool.jar

to the end of the CLASSPATH variable. The procedure is similar for UNIX except that individual paths within the CLASSPATH environment variable is separated by a colon not a semi-colon.

Execution

The GMV tool a can rundirectly from this web site via an applet which is accessible from the GMV Tool Page. However, running the tool from the applet will result in slower execution time and a number of restrictions imposed by your web browser. These restrictions mean that some of the options listed below are not available to the tool when run from a web browser. By installing the software on your local machine it is possible to avoid many of these restrictions and to significantly increase execution time of the program. The software can be downloaded from the GMV Tool Page.

If you have downloaded and installed the GMV software and possess a Java interpreter, such as Sun's JRE then you can run the GMV tool as an application on your machine with no restrictions. To run the application simply type at your command prompt

Java uk.ac.CropNet.GMV.GMVApplication [file-name]

where [file-name] is an optional parameter indicating a comparative genome map which has been saved from a previous session. Alternatively you can also use the 'GMVTool' script that is provided with the distribution, which does basically the same thing, by typing

Java uk.ac.CropNet.GMV.GMVApplication [file-name]

Alernatively, if you are using JRE version 1.2 at the command line type the following

Java -jar GMVTool.jar

or if you are using MS windows NT/98 you need only double click on the archive file.

Menu commands

When the GMV tool is executed an application style window appears that contains a menu bar containing the following menus.

File menu

• New Currently not used, but reserved for latter use.
• *Open... Loads a circular genome map from your local file system.
• *Save Saves the currently loaded comparative genome map as the file current file name. If no file name has been defined then a 'save file' dialog will open. Please use the .gmv extension to denote these files. An example file (example.gmv file included in the distribution.
• *Save as... Opens a Saves 'save file' dialogue and allows you to define the name of the file to which the current comparative genome map will be saved. Please use the .gmv extension to denote these files.
• **Print... Will print the current comparative genome map. In the current version of the GMV tool you will be warned if the print size is too small for the paper, which will allow the you to manually zoom the image so that it will fit the page. In latter versions a option will be available for this to be performed automatically.
• Close Will close the current comparative genome map, but you will be asked if the map has not been saved whether the map should be saved before closing.
• Exit Will exit the GMV Tool but if map is being display and has not been saved, you will asked, if the map has not been saved, whether the map should be saved before exiting.*Only available if running from an application or from a non-Netscape browser using an applet loaded from your local file system.
  **Not available if run as an applet.

Import/Export menu

Import... This command will open the above dialogue to allow you to choose from import data from a text file or a database.

• From a ACEDB database. Choosing this option will allow you to import data from any of the ACEDB databases available on the currently configured CITA server. For details on how to change the current server look at the please check the README file that is provided with the software distribution. The GMV Tool can import genome blocks with or without loci. See the section of 'Importing data from a ACEDB database'
• From a ace file The GMV Tool can read text files rewritten in ace format, which is the format normally used for add data to ACEDB. See the documentation on ACEDB at http://www.sanger.ac.uk/Software/Acedb/ or look at the example.ace file included in the distribution. Later versions will provide you with a choice of file formats and database systems.

Export... allows you to export the genome maps as a text file. Currently only ace file format is supported but later versions will provide you with a choice of file formats.

Windows menu

• Key will open the key display which is described in the Display section
• is also described in the display section

Display menu

This menu is only enabled when a comparative genome map is displayed. The menu is a collection of checkable items that allow you to switch on specific parts of the display to increase or decrease its detail. The following switches are available.

• Show Full Details
• Reset To Default
• Genome Blocks
  This sub-menu is a collection of checkable items that allow you to choose which of the currently loaded genome blocks should be displayed.
• Show Chromosome Block Names
• Show Full Names
• Show Block Names
• Show Individual Blocks
• Show Chromosome Block End Labels
• Show Centromeres
• Show Telomeres
• Show Possible Translocations
• Show Possible Inversions
• Show Poorly Mapped Regions
• Show Loci
• Show Chromosome Block Dividers

Help menu

• Help... Will open a help dialogue which in future version will display more comprehensive help items, but in this version displays similar data to that obtained by the About Dialogue.
• About... Will open an About Dialogue showing information about the GMV Tool
• Copyright... Will open an Copyright Dialogue showing the GCMQ Tool copyright information.

Importing data from a ACEDB database

When the 'import from ACEDB' option is choose you are presented with another dialogue box (see picture above), which allows to choose whether to import genome blocks alone or with loci mapped on to them.

In the next dialogue box (see picture above) you are asked from which database you wish to import the data.

The next dialogue box (see picture above) asks you to choose which genome blocks to import.

Next if you choose 'genome blocks with loci then you are presented with yet another dialogue box (see picture above) which asks you to choose which loci to map on to the genome blocks. Only those loci which map on to the genome blocks you choose will be listed. If you select the 'import homologous loci' option then all the loci that are homologous to the loci you choose and which also map on to the genome blocks you choose will also be imported.

The viewer will now request the require data from the database and display it as a circular genome maps.

Displays

Main (comparative genome map)display

The comparative genome map fills the main part of the application window and clicking on the maps will bring up the information display giving further details. The display contains scroll bars (the inner two bars indicated in the above picture) which can be used to centre on different parts of the display. On the right of the display is the zoom bar (see above picture), which can used to increase or decrease the size of the display. It will not change the size of actual window, which be adjusted in the same you would adjust the window on your system. At the bottom of the display is the rotation bar which can be used to rotate the genome maps.

Key Display

The key display provides details about the symbols used on the genome map display and a colour code for the genome blocks displayed.

Information Display

The information display provides information specific to the genome maps being displayed. Two examples of this display are shown above. Text highlighted in blue are hyperlinks to further information.

Designed and maintained by Virginia Barnard
LAST UPDATED: 21st September 2005