REGENDER: REsident GENome DEtectoR

This is the companion web site of the REGENDER tool. Follow the links below to download the high-resolution versions of the plots referred in the paper. The Saccaromices Cerevisiae dataset (Liti et al., 2009) can be downloaded from here. Since REGENDER take as input plain text files, the download files must be converted into plain text sequences to be used (read readme.txt in the REGENDER zip file for more info). The strains Y55 and YPS128, are already included in the REGENDER zip file.

Requirements

• Java(>=6) + Fastutil 5.1.5

• Python (>=1.6) + Matplotlib

• Bash (the Windows users are recommended to download Cygwin)

(The Java, Python, and the Bash interpreter are required to be in the system path)

Installation

1. Download REGENDER

2. Unzip regender.zip into the "regender" dir.

3. Download the Fastutil library, moving the "fastutil-5.1.5.jar" file in "regender/lib".

4. Change dir to "regender/py" and run the REGENDER tool, specifying: the name of the strain to analyze, the size of the l-grams, and the delta1/delta2 thresholds (e.g. "python regender.py y55 32 100 100" .) The output is written in "regender/out/y55".

References

G. Menconi, G. Battaglia, R. Grossi, N. Pisanti and R. Marangoni.
Mobilome inference in yeast genomes.
Poster at BITS 2010. (Extended version submitted for publication)

G. Battaglia, R. Grossi, N. Pisanti, R. Marangoni, and G. Menconi.
Inferring Mobile Elements in S.Cerevisiae strains.
Proc. International Conference on Bioinformatics Models, Methods and Algorithms (BIOINFORMATICS)
SciTePress pages 131-136, 2011

Links

• Plots
• REGENDER Executable
• Experimental comparison between REGENDER and other existing tools
• Dataset by Liti et al. (note that it must be preprocessed)