File	Date	Author	Commit
t	2013-07-18	ctSkennerton	[26d6df] Initial commit
CHANGES	2013-11-19	ctSkennerton	[29dbe2] Fixed bug in gff output causing header to be pr...
CRISPR.java	2013-11-18	ctSkennerton	[6cb89d] Added in new output formats
CRISPRFinder.java	2013-11-19	ctSkennerton	[29dbe2] Fixed bug in gff output causing header to be pr...
CRISPRUtil.java	2013-07-18	ctSkennerton	[26d6df] Initial commit
DNASequence.java	2013-07-18	ctSkennerton	[26d6df] Initial commit
FASTAReader.java	2013-07-18	ctSkennerton	[26d6df] Initial commit
LICENSE	2013-07-18	ctSkennerton	[26d6df] Initial commit
MANIFEST.txt	2013-11-18	ctSkennerton	[6bdc6f] Added in a manifest file and a makefile for com...
Makefile	2013-11-18	ctSkennerton	[6bdc6f] Added in a manifest file and a makefile for com...
README	2013-07-18	ctSkennerton	[26d6df] Initial commit
SearchUtil.java	2013-07-18	ctSkennerton	[26d6df] Initial commit
minced	2013-11-18	ctSkennerton	[f47d00] Added in a shell wrapper for the jar file
minced.java	2013-11-19	ctSkennerton	[29dbe2] Fixed bug in gff output causing header to be pr...

Read Me

MinCED - Mining CRISPRs in Environmental Datasets


MinCED is a program to find Clustered Regularly Interspaced Short Palindromic
Repeats (CRISPRs) in full genomes or environmental datasets such as metagenomes,
in which sequence size can be anywhere from 100 to 800 bp. MinCED runs from the
command-line and was derived from CRT (http://www.room220.com/crt/):
  Charles Bland et al., CRISPR Recognition Tool (CRT): a tool for automatic
  detection of clustered regularly interspaced palindromic repeats, BMC
  Bioinformatics 8, no. 1 (2007): 209.


INSTALLATION

You need to install these dependencies first:
  * Java (http://www.java.com/en/download/)

In the MinCED folder, compile the source files: 
  * javac  *.java

To run MinCED, in the same folder:
  * java minced [options] inputFile [outputFile]

The help page can be obtained by typing:
  * java minced --help

You can get the MinCED version this way:
  * java minced --version


EXAMPLES

Finding CRISPRs in the E. coli genome:
    java minced ecoli.fna

To find repeats in short sequences, we need to decrease the minimum number of
repeats to find. For example, in 100 bp reads, we could not possibly find more
than 2 repeats:
    java minced -minNR 2 metagenome.fna

The output can be large, so save it in a file:
    java minced -minNR 2 metagenome.fna metagenome.crisprs

COPYRIGHT AND LICENSE

Copyright 2011 Florent ANGLY <florent.angly@gmail.com>

MinCED is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.
MinCED is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
GNU General Public License for more details.
You should have received a copy of the GNU General Public License
along with MinCED.  If not, see <http://www.gnu.org/licenses/>.


BUGS

All complex software has bugs lurking in it, and this program is no exception.
If you find a bug please email me at <florent.angly@gmail.com> so that I can
make MinCED better.