Sole-Search tool: Determines statistically significant peaks from ChIP experiments sequenced by an Illumina Genome Analyzer (ChIP-Seq). This analysis software includes a primary background model, representing mappable and sequenceable regions of the genome, for determining peak height cutoff by false discovery rate. It also includes several secondary background models from which to choose or an option to enter your own input file, for determining significance over a cell type-specific background. Finally, it determines duplication and deletion events within the cell type of interest and separates peaks found within duplicated regions for further scrutiny by the scientist. Output from the Illumina Genome Analyzer is processed. Software produces run statistics, visualization file of raw data, and significant peaks files, as determined by the three-pass model.
GFF-Overlap tool: Determines overlap of binding sites between two data sets. User can compare two peak files in GFF format from either ChIP-Chip arrays, ChIP-Seq experiments or a combination of the two. The software determines the overlap between the two files with allotted gap; peaks can overlap completely, or overlap can be determined based on a user-defined gap between peaks. Output is an overlap file, a no overlap file, and a union file, in GFF format.
Location-Analysis tool: Determines location of a binding site, from a peak file in GFF format, with respect to the nearest gene. Output of the software gives the name and coordinates of the gene nearest the binding site, distance from TSS, gene annotation where applicable, etc.
