p53scan & p63scan: search for the p53 or p63 motif

p53scan is an algorithm to search for p53 consensus binding motif, as determined in a genome-wide ChIP-chip study, in DNA sequences. The same algorithm has also been combined with the p63 binding motif obtained from a genome-wide p63 ChIP-seq study in human keratinocytes to form p63scan.

Usage

p53scan and p63scan will run with the default options (optimized cutoffs, spacer 0-13 for p53scan, spacer 0 for p63scan) when no other options are specified. If the spacer length is specified, but no cutoff is set, then all matches up to a maximum of nreport are shown. Both p53scan and p63scan accept the same command-line arguments.

Input is a FASTA-formatted file, output is a GFF file.

Command-line version

p53scan.py -i <FILE> [optional arguments]
or
p63scan.py -i <FILE> [optional arguments]

Options

--versionshow program's version number and exit
-h, --helpshow this help message and exit
-i FILE, --input=FILEFASTA-formatted inputfile
-n N, --nreport=Nreport maximum N matches
-p FILE, --pwm=FILEspecify your own PWM file
-s L, --spacer=Luse spacer length L (either specify one spacer, or use the format min-max)
-c C, --cutoff=Ccutoff or comma-separated list of cutoffs, one for each spacer length

Example

p53scan.py -i p53_targets.fa -s 0-1 -c 4.39,13.7 -n 5

Scan the file p53_targets.fa for binding motifs. All matches with a spacer of 0 and a score higher than 4.39 are considered, as well as all matches with a spacer of 1 and a score higher than 13.7. A maximum of 5 matches are reported per sequence.

Custom PWM-file

It is possible to specify your own PWM-file for use with p53scan. This file should contain two matrices, one for each half-site. An example of the required format is shown below. This file should be tab-separated, with each line containing the frequencies of A,C,G and T (in that specific order). Please note that the cutoffs provided by p53scan are highly optimized for p53. p53scan will use a threshold score of 0.85 * maximum_score of your provided motif by default. Tweaking this score might greatly improve the sensitivity/specificity balance of your results.

Example PWM-file:

>ER_left
0.588 0.061 0.359 0.008
0.061 0.015 0.817 0.122
0.008 0.008 0.977 0.023
0.023 0.046 0.137 0.809
0.008 0.931 0.031 0.046
0.916 0.008 0.038 0.053
0.076 0.496 0.344 0.099
>ER_right
0.107 0.313 0.473 0.122
0.008 0.046 0.008 0.954
0.038 0.046 0.924 0.008
0.748 0.198 0.031 0.038
0.023 0.977 0.008 0.008
0.115 0.779 0.015 0.107

Downloads

p53scan code is freely available under terms of the MIT license. If you publish results obtained with p53scan or p63scan, we would greatly appreciate it if you would cite the refences provided below.

Latest version: 1.05

Changelog 2010-06-21 Changelog 2009-05-13

Linux

Download source tarball: p53scan-1.05.tar.gz

Unpack this archive with tar -vxzf p53scan-1.05.tar.gz. Change to the p53scan-1.05 directory and run the following commands:

   python setup.py build
   python setup.py install (superuser access required)

This will install the p53scan python module. The scripts to run p53scan (p53scan.py for the command-line version and p53scan_gui.py for a simple graphical interface) will be installed in /usr/bin/

Windows (32-bit)

Version 2.5 of Python is required to use this installer.

Download binary installer: p53scan-1.05.win32-py2.5.zip

By default a shortcut to the GUI version of p53scan will installed. The command line version is also available, and will be located in the Scripts folder of your Python installation.

Other platforms

If you have Python and a C-compiler you should be able to use the source package, although this has not been tested.

Contact

For questions, suggestions or bug reports please contact Simon van Heeringen: s.vanheeringen@ncmls.ru.nl

References

p53scan

Smeenk L, van Heeringen SJ, Koeppel M, Driel MA, Bartels SJ et al. Characterization of genome-wide p53-binding sites upon stress response. Nucleic Acids Research. (2008)

p63scan

Kouwenhoven EN, van Heeringen SJ, Tena JJ, Oti M, Dutilh BE et al. Genome-wide profiling of p63 DNA-binding sites identifies an element that regulates gene expression during limb development in the 7q21 SHFM1 locus. PLoS Genetics. (2010)
RU horblack (1K)

Nijmegen Center for Molecular Life Sciences Faculty of Science Radboud University Nijmegen