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Accueil > Research > TALLA > Software > VisualModuleOrganizer

VisualModuleOrganizer

by Talla Emmanuel -

Visual ModuleOrganizer version 1.0

ModuleOrganizer detects repeated modules in sequences and allows comparative and evolutionary analysis of these elements. It was recoded in C++ and optimized for larger sequences. Visual ModuleOrganizer is a JAVA graphical interface that displays graphical results from the new embedded version of ModuleOrganizer and allows easy handling of the results.


Installation instructions and Use of ModuleOrganizer
- Download 64-bit ModuleOrganizer binaries (Windows, MacOs and Linux) in a given directory (for example : the Desktop directory) here .
 Be careful, you must download the file, do not open it !
- Unzip the zipped files (Winzip, unzip, ...) in the Desktop directory.
 Note a ModuleOrganizer2 directory must be created in the Desktop directory
- Open a terminal :
 for Windows user : Click on "Start > All Programs > Accessories > Command Prompt"
 for MacOS user : Click on "Applications > Utilities > Terminal"
- Go to the Desktop directory with the opened terminal :
 for Windows user, tape : "cd Desktop\ModuleOrganizer2"
 for MasOs and Linux user, tape : "cd Desktop/ModuleOrganizer2"
- In the terminal prompt, tape :
 for Windows user : "ModuleOrganizer2.win32.exe"
 for MacOS user : "./ModuleOrganizer2.MacOs"
 for Linux user : "./ModuleOrganizer2.linux"
- If a text describing the ModuleOrganizer2 usage is printed, the software works. Otherwise, the file is not executable, check the permission file.
- Now you can use ModuleOrganizer2 with the example files described below or use your own sequence(s) in FASTA format file.


Installation instructions and Use of Visual ModuleOrganizer
- Download Visual ModuleOrganizer in a given directory (for example : the Desktop directory) here.
 Be careful, you must download the file, do not open it !
- Unzip the zipped file (Winzip, unzip, ...) in the Desktop directory.
 Note a VisualModuleOrganizer directory must be created in the Desktop directory
- Open a terminal :
 for Windows user : Click on "Start > All Programs > Accessories > Command Prompt"
 for MacOS user : Click on "Applications > Utilities > Terminal"
- Go to the Desktop directory with the opened terminal :
 for Windows user, tape : "cd Desktop\VisualModuleOrganizer"
 for MasOs and Linux user, tape : "cd Desktop/VisualModuleOrganizer"
- In the terminal prompt, tape :
 for Windows user : "ModuleOrganizer2\ModuleOrganizer2.win32.exe"
 for Mac user :"./ModuleOrganizer2/ModuleOrganizer2.MacOs"
 for Linux user : "./ModuleOrganizer2/ModuleOrganizer2.linux"
- If a text describing the ModuleOrganizer2 usage is printed, the software works. Otherwise, the file is not executable, check the permission file.
- In the terminal prompt, tape : "java -jar VisualModuleOrganizer.jar", if a interface opens, you can use VisualModuleOrganizer ; otherwise you do not have JAVA on your computer (you must install it) or your JAVA version is too old, you need to update it (VisualModuleOrganizer was compiled with JAVA 1.6).
- If you use Window or MacOS, you can double click on the JAR file from the Desktop to open the interface.
- Now you can use VisualModuleOrganizer with the example files described below or use your own sequence(s) in FASTA format file.


Examples of input sequences
- Data set used for (time and memory) comparison of the old ModuleOrganizer and the new ModuleOrganizer version are available here
(FASTA sequences : comparison*kb.fasta).
- Artificial annotated set of sequences (ModuleOrganizer results : test.txt, test.txt.upgma and test.txt.vmo ; and corresponding annotations : SEQ1_Genbank.gbk, SEQ1_Censor.map, SEQ1_myTEAnnot.txt, SEQ2_Censor.map, SEQ2_BLAST.out, SEQ3_myAnnotation.txt and SEQ3_RepeatMasker.out) are available here.
- Foldback4 sequences (FASTA sequences) is available here.