The Peak Fitting ChIP-chip analyzing algorithm

1. Transcription factors (green) bind sequence-specific sites at the promoters of their target genes.

2. Using sonication, the DNA is sheared into ~500bp-long fragments, and immunoprecipitated.

3. Probes closer to the binding position are more enriched with IPed DNA, following a peak-like shape

4. The expected shape of the peak can be derived from the distribution of DNA fragments

5. Examples of single-site promoters (YGR243W IPed for Sko1)

6. Or multiple-site promoters (YLR412C-A, YOR028C IPed for Sko1 at no salt)

The PeakFitting algorithm is freely available for the purpose of performing non-commercial academic research, from here.
Please cite Capaldi et al., Structure and Function of a Transcriptional Network Activated by the MAPK Hog1, Nature Genetics, 2008, 40:1300-6

For all other purposes, please contact Prof. Nir Friedman and Dr. Tommy Kaplan at peakfit@cs.huji.ac.il