An integrated genome and ortholog viewer (inGeno) is designed for genome sequence comparisons, which has been proven to be powerful, in particular to prokaryotic genomes of close phylogenetic distances. The original purpose of this software is to user-friendly visualize the corresponding relationships between orthologous genes. Step by step, a series of algorithms are implemented and integrated together, thus enable a noise-reducing process, a locus collinear block recognition and a text-mining step, which are helpful for users to extract biological information precisely.

This part is specially prepared for our students as a practice to acquire a quick impression of pairwise genome comparisons, through the sample files, people could notice easily the strain-specific genes in red color, the potential operons present in the genome, foreign insertion caused by phage and many rearrangement events.

Package

The practice package can be fetched HERE , which includes a lot of demo snapshot files, i.e., strain comparison results between Listeria, Staphylococcus, Blochmannia and E. coli species.

Steps

1. unpack the downloaded package, run it by simply clicking the executable file "ingeno.bat "(WIN) or typing "./ingeno" (LIN).

2. within inGeno, the menu "File" / "Restore from a snapshot" is designed for importing these snapshot files. Afterwards, users please sequentially click the buttons "Dotplot" and "Compare", the comparison figures will be generated in the screen. -Recommended Demo file is currently located at ./SampleData/Listeria/lmolwe.snapshot and ./SampleData/Listeria/lmolin.snapshot

3. in the panel, there are operation controls for helping users to optimize the view, e.g., zoom, distance, color clusters, thresholds. Moreover, mouse operations are allowed to be applied directly on the gene position and observe the corresponding information.

4. comparison from original files. Download the genome genbank files (lmo.genbank, lin.genbank) from the "SAMPLE FILES" below. Blast them with appropriate parameters and collect the reports. Or for convenience, download two reports (lmolin.report, linlmo.report), which are pairwise comparison for eliminating the false-negative noises. Load them (4 FILES) into inGeno software, note you have to upload all these files together in the "Import data from disk" window. Then you couldperform the comparison function.

 2006.12 ingeno 0.6 available (stable)

 2006.3 ingeno 0.5 available
 2006.2 ingeno 0.4 available
 2006.1 ingeno 0.3 available
 2005.12 ingeno 0.2 available
 2005.10 ingeno 0.1 available

Program

(JarRAR file is a package file suitable for most users, users could unpack it, then execute it by ingeno.bat or ./ingeno)

Tutorial

The latest version of supplementary material can be downloaded here, including a PDF document. Users can get instructions how to initiate the program, download and import a sequence file or data mirror, further analyze it using the interactive interface. A couple of sample files are also downloadable, which are helpful for new users to get fit of the software.

       Supplementary material updated in July, 2006

Pentium CPU compatible or higher, 256M RAM is recommended. When the genome size is large than 5,000,000 BP, 512M or higher is optimal for obtaining a satisfied speed. A  JRE environment 1.5 or later version is demanded, since it is completely implemented in Java, the program can run properly on a various platforms (Linux/Windows-stable-,  MAC platforms-unaccomplished).

Here are some screenshots of the inGeno, which illustrate some features and applications useful for studing genome information, such as linear conservation, rearrangement events, phylogenetic evolution, specific functions which are necessary for reconstructing the metabolism. All the figures are taken from inGeno Ver 0.5a.

Figure 1. Typically investigation grahpic user interface (GUI). Detail description please read supplemenary materials.

 

Analysis Example Screenshots

I. Visualization a strain-specific gene islands, which enable a novel metabolism pathway. These genes are continuous in genome, which might to form an operon (Potential operon detection sample (a strain-specific gene island), click to view large figure

     

  

II. Genome rearrangment events investigation samples (green lines in figure), LCB defined by color clusters.

   

Copyright by Dandekar Group, Bioinformatik, Uni Wuerzburg, 2006
All rights reservered.