Please cite:
P. E. Warburton, J. Giordano, F. Cheung, Y. Gelfand and G. Benson.
"Inverted Repeat Structure of the Human Genome:
The X-Chromosome Contains a Preponderance of Large,
Highly Homologous Inverted Repeats That Contain Testes Genes" ,
Genome Research, 14:1861-1869, 2004.
This program is a command line version of the IRF algorithm used to investigate inverted repeat structure of the Human henome in the paper above. We are currently in the process of improving the algorithm with the following: removing size limitations on stem and loop, doing statistical analysis of biologically common inverted repeats, using multihit strategies with regular or indel seeds, etc.
Please pay special attention to -t4,-t5,-t7 parameters which directly control lookback distances.
Example of input
irf.exe 3582.7968871.4281.IRDB.txt 2 3 5 80 10 40 500000 10000 -d -h -t4 74 -t5 493 -t7 10000
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