Sole-Search tool: Determines statistically significant peaks from ChIP experiments sequenced by an Illumina Genome Analyzer (ChIP-Seq). This analysis software 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. It determines duplication and deletion events within the cell type of interest, as well as regions of sequence bias, and normalized the ChIP-seq sample. Peak height cutoff is determined based on a user-defined FDR. A new option allows the user to more easily and accurately determine regions of histone modifications. Output from the Illumina Genome Analyzer is processed. Software produces run statistics, visualization files of raw data, and a significant peaks file.
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.
GFF-to-FASTA tool: Gives the user sequence information in FASTA format for any file in GFF format. FASTA file can then be used in an external motif-calling program.
