Motivation: Clusters of protein–DNA interaction events involving the same transcription factor are known to act as key components of invertebrate and mammalian promoters and enhancers. However, detecting closely spaced homotypic events from ChIP-Seq data is challenging because random variation in the ChIP fragmentation process obscures event locations.#R##N##R##N#Results: The Genome Positioning System (GPS) can predict protein–DNA interaction events at high spatial resolution from ChIP-Seq data, while retaining the ability to resolve closely spaced events that appear as a single cluster of reads. GPS models observed reads using a complexity penalized mixture model and efficiently predicts event locations with a segmented EM algorithm. An optional mode permits GPS to align common events across distinct experiments. GPS detects more joint events in synthetic and actual ChIP-Seq data and has superior spatial resolution when compared with other methods. In addition, the specificity and sensitivity of GPS are superior to or comparable with other methods.#R##N##R##N#Availability: http://cgs.csail.mit.edu/gps #R##N##R##N#Contact:gifford@mit.edu; mahony@mit.edu#R##N##R##N#Supplementary information:Supplementary data are available at Bioinformatics online.
['Yuchun Guo', 'Georgios Papachristoudis', 'Robert C. Altshuler', 'Georg K. Gerber', 'Tommi S. Jaakkola', 'David K. Gifford', 'Shaun Mahony']
Discovering homotypic binding events at high spatial resolution