PRAP: An ab initio Software Package for Automated Genome Wide Analysis of DNA Repeats for Prokaryotes
Gwo-Liang Chen1, Yun-Juan Chang2 and Chun-Hway Hsueh1*
1Department of Materials Science and Engineering, National Taiwan University, Taipei 10617, Taiwan.
2HPCBio, the University of Illinois, 1206 W. Gregory Drive, Urbana, IL 61801, USA
Introduction
PRAP (Prokaryotic Repeats Annotation Program) is a software package to automate the analysis of repeats in both finished and drafted genomes.It aimed at identifying full spectrum repeats at the prokaryote genome scale.
The final output is parsed into the EMBL/GenBank feature table format for reading and displaying in Artemis, where it can be combined or compared with other genome data. It is currently the most complete repeat finder for prokaryote and is a valuable tool for the annotation.
Download and install
Right click the link to download PRAP(link) (.zip)
Click the link to download PRAP(link) (.tar.gz)
The READ_ME file is included to explain how to install and run PRAP what each part of the program does.
The code was written in Perl and run on UNIX. In order to run the code,
Perl Interpreter 5.6.1 or later (http://www.perl.org/),
MegaBLAST/blastn (http://www.ncbi.nlm.nih.gov/BLAST/),
RECON (http://selab.janelia.org/recon.html),
VisCoSe (http://bio.math-inf.uni-greifswald.de/viscose/html/download.html),
RepeatMasker (http://www.repeatmasker.org/) and
Artemis (http://www.sanger.ac.uk/Software/Artemis/)
are required by users and all codes must be installed in the user’s execution path.
License
This program is free software and is distributed under
the term of the GNU General Public License (version 3) as published by
the Free Software Foundation.
Contact
If you have any questions, please PRAP Software, Contact Dr. Gwo-Liang Chen (glchen@ntu.edu.tw) | 