IRF - Inverted Repeats Finder

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

Example of output.

Version 3.07 Downloads:

(added -ngs flag for more compact .dat output on multisequence files, returns 0 on success.)

    Windows Command Line Version

    Linux on PC compatible

Version 3.05 Downloads:

Please Select your system type:

    Windows Command Line Version

    Linux on PC compatible

    Mac OS on PC compatible

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Last revised February 18, 2015
Send any questions or comments to:
Yozen Hernandez