ott@rockefeller.edu

- Line 1: Number of order statistics to evaluate (may be 0)
- Line 2: Number of bootstrap replicates to carry out. Set to 0 for none.
- Line 3: Threshold limits (%max) for evaluating significance levels of scores at or above these thresholds. List any number of limits, no trailing text. Whole numbers only. Leave blank for no limits. Is relevant only for a value >0 on line 2.
- Line 4: Gap weights (1) or no gap weights (0). With gaps weight on, scores will be weighted by relative frequency of gaps in the genome (up to gap (spacer) length of 14.
- Line 5: Smoothing factor for gap weight (0 for no smoothing; no effect when gap weights are off)
- Line 6: Multiplier for score contributions of core sites, #4 - #7, #14 - #17
- Line 7: Use filtering (1) or not (0)
- Line 8: Smoothing constant s in log likelihood ratio score, ln(LR + s). A value of -1 indicates that s will be chosen so highest and lowest scores will be equal in absolute value.
- Line 9: Scoring method, likelihood ratio (1) or conditional probability (0)
- Line 10 (two numbers):
- n1 = Number of bp to skip before reading sequence (may be 0)
- n2 = Number of bp to read (after skipping) in given gene (0 for whole gene). For example, if n1 = 1000 and n2 = 12000, then reading the gene sequence would start at position 1001 and would continue for 12000 nucleotides. On output the actual sequence positions in the gene are given.
- Line 11: Print 15 bp of sequence flanking the putative binding site (1) or not (0)
- Line 12: Number of gap sizes to test. Two options (choose one or the other, no trailing text):
- -1 n indicates that scores should be maximized over gap sizes from 0 through n (max for n = 20), or
- n1 n2 ... provides a list of gap sizes to test. There must be at least one number.

- Traditional approach. Open a command window (“DOS box”) and change directories until you are in the directory (folder) where the p53MH program and its files reside. Then enter the command, p53MH.
- Double click on the p53MH (p53MH.exe) file. The program will then execute and show progress on screen. Once it finishes the window closes automatically. Alternatively, to execute the program and save screen output to a file, double click on the run (run.bat) file. After the program finishes, screen output may be viewed by inspecting the screen.out file.

- p53res.out presents detailed output
- p53ord.out essentially provides the same output as above but in a format that is easy to import into a spreadsheet
- p53psum.out: If computer simulation is requested (input line 2) then this file is written and contains p-values for sums of order statistics for the scores.
- p53pmin.out: Analogous output for minimum p-value for sums of order statistics (one result per gene)

[2] Perez CA, Ott J, Mays DJ, Pietenpol JA (2007) p63 consensus DNA-binding site: identification, analysis and application into a p63MH algorithm. Oncogene 26, 7363-7370