Package Name: DGRscan
First Released on June 15, 2014
Developer: Yuzhen Ye <yye@indiana.edu>
Affiliation: School of Informatics and Computing, Indiana University, Bloomington

The development of DGRscan was supported by NSF grants DBI-0845685 and DBI-1262588

DGRscan is free software under the terms of the GNU General Public License as published by 
the Free Software Foundation.

>> Introduction

DGRscan is a tool for identification of DGR systems from genomic sequences, which can be
whole genomes, contigs, or even short reads.

DGRscan is written in python, so it is ready to run

>> What's in the package

DGRscan.py -- the main python program
data -- the data folder, which contains known reverse transcriptases (RT) and known template sequences (TR)
tests -- the folder with example sequences for testing the program

>> Third party programs that might be needed
DGRscan.py does not rely on any third party software; 
however, if you want to use RT/TR predictions to constrain/guide the prediction, 
you need to use the BLAST suite for the similarity searches. 

>> Using DGRscan
DGRscan supports de novo predictions or similarity search based predictions of DGR systems.
Usage: type ./DGRscan for usages

>> Examples (under tests/ folder)

You may call a simple script (commands.sh) under tests/ folder to run all three tests:

A little more details on the tests:

Example 1: De novo prediction in a short input genomic sequence
Input sequence file: small.seq
Command:
../DGRscan.py -inseq small.seq -summary small-DGRscan.summary
Note: DGRscan should report a potential TR-VR pair in this sequence

Example 2: De novo prediction of DGR system in a complete genome using RT predictions to constrain the search space
Input sequence: FQ312004.fna ( Bacteroides fragilis 638R genome)
Command:
../DGRscan.py -inseq FQ312004.fna -summary FQ312004-DGRscan.summary -rev_hom FQ312004-vs-RT155.m8
(Note: FQ312004-vs-RT155.m8 is the blastall or blastx results of potential RTs)

Example 3: Similarity search based predictions of DGR systems
Input sequence: FQ312004.fna
Command:
../DGRscan.py -inseq FQ312004.fna -summary FQ312004-DGRscan-hom.summary -tr_hom FQ312004-vs-TR.m8
(Note: FQ312004-vs-TR.m8 is the blastall or blastn results of potential TRs & VRs)