Readme file for metaCRT & summarize-crispr-new.py

Yuzhen Ye (yye@indiana.edu, yuzhenye@gmail.com)
School of Informatics and Computing, IUB

** metaCRT **

modified from CRT1.2 (CRT1.2 was downloaded from http://www.room220.com/crt/, by Bland et al)

What's new in metaCRT: allowing multiple sequences & incomplete repeats at the ends
(Want to apply other criteria? Check summarize-crispr-new.py at the end of this file)

Setup & use metaCRT

1. compile java codes:
javac *.java

2. prepare a package
jar cvf metaCRT.jar *.class

(rename the package as metaCRT.jar)

3. use the package:
java -cp metaCRT.jar crt fastafile output 

example:
java -cp metaCRT.jar crt SRS024075_LANL.contigs.fa SRS024075_LANL.contigs.fa-crt.out


** summarize-crispr-new.py **
A python script to apply other criteria for further filtering CRISPRs
