IRF - Inverted Repeats Finder

Using Command Line Version of Inverted Repeats Finder

Once the program is installed you can run it with no parameters to obtain information on proper usage syntax.

example: irf3.exe Human21.fa 2 3 5 80 10 40 100000 500000 -t7 600000 -d -l

Things to note:

1. This will use matching parameters +2,-3,-5 for a minimum score of 40
2. a max buffer of 100K will be used for stems
3. tuple of length 7 (least sensitive) will look at most 600K back
4. anything over 500K loop will be removed.
5. lowercase letter will be ignored during detection phase

usage: irfprogram File Match Mismatch Delta PM PI Minscore Maxlength MaxLoop [options]

Where: (all weights, penalties, and scores are positive)
  File = sequences input file
  Match  = matching weight
  Mismatch  = mismatching penalty
  Delta = indel penalty
  PM = match probability (whole number)
  PI = indel probability (whole number)
  Minscore = minimum alignment score to report
  MaxLength = maximum stem length to report (10,000 minimum and no upper limit, but system will run out memory if this is too large)
  MaxLoop = filters results to have loop less than this value (will not give you more results unless you increase -t4,-t4,-t7 as well)
  [options] = one or more of the following :
               -m    masked sequence file
               -f    flanking sequence
               -d    data file
               -h    suppress HTML output (this automatically switches -d to ON)

               -l    lowercase letters do not participate in a k-tuple match, but can be part of an alignment
               -gt   allow the GT match (gt matching weight must follow immediately after the switch)
               -mr   target is mirror repeats
               -r    set the identity value of the redundancy algorithm (value 60 to 100 must follow immediately after the switch)

               -la   lookahead test enabled. Results are slightly different as a repeat might be found at a different interval. Faster.
               -a3   perform a third alignment going inward. Produces longer or better alignments. Slower.
               -a4   same as a3 but alignment is of maximum narrowband width. Slightly better results than a3. Much slower.
               -i1   Do not stop once a repeat is found at a certain interval and try larger intervals at nearby centers. Better(?) results. Slower.
               -i2   Do not stop once a repeat is found at a certain interval and try all intervals at same and nearby centers. Better(?) results. Much slower.
               -r0   do not eliminate redundancy from the output
               -r2   modified redundancy algorithm, does not remove stuff which is redundant to redundant. Slower and not good for TA repeat regions, would not leave the largest, but a whole bunch.

               -t4   set the maximum loop separation for tuple of length4 (default 154, separation <=1,000 must follow)
               -t5   set the maximum loop separation for tuple of length5 (default 813, separation <=10,000 must follow)
               -t7   set the maximum loop separation for tuple of length7 (default 14800, limited by your system's memory, make sure you increase maxloop to the same value)

               -ngs  more compact .dat output on multisequence files, returns 0 on success.

Note the sequence file should be in FASTA format:

>Name of sequence
   aggaaacctg ccatggcctc ctggtgagct gtcctcatcc actgctcgct gcctctccag
   atactctgac ccatggatcc cctgggtgca gccaagccac aatggccatg gcgccgctgt
   actcccaccc gccccaccct cctgatcctg ctatggacat ggcctttcca catccctgtg