Arpeggio

Researchers generating new genome-wide data in an exploratory sequencing study can gain biological insights by comparing their data with well-annotated datasets possessing similar genomic patterns. Data compression techniques are needed for efficient comparisons of a new genomic experiment to large repositories of publicly available profiles.

Arpeggio allows us to efficiently compare numerous ChIP-seq datasets consisting of many types of DNA-binding proteins collected from a variety of cells, conditions and organisms. Importantly, these interaction patterns broadly reflect the biological properties of the binding events. To generate these profiles, termed Arpeggio profiles, we applied harmonic deconvolution techniques to the autocorrelation profiles of the ChIP-seq signals.

A detailed tutorial is available in the Wiki page (http://sourceforge.net/p/arpeggio/wiki/Home/)