CSI-ANN allows the user to predict regulatory DNA elements using chromatin modification data. The user provides chromatin modification data (e.g., H3K4me1, H3K4me3, H3K27ac, etc), either ChIP-chip or ChIP-Seq, and the sotfware produces a text file containing the prediction centers of regulatory DNA elements (genomic positions) across the regions/genomes.

The CSI-ANN framework consists of a data transformation and a feature extraction step followed by a classification step using Time-Delay Neural Network (TDNN). Chromatin modification data can be used directly by the software (i.e. using summary statistic in a window) or processed through a pre-processing step to generate additional features (e.g., statistical measures such as variance, kustosis). Input Data are provided to the software in a prespecified format (see T cell sample files provided). The software is written in C.