Fig. 1

Flowchart of the PATTERNS period calculation procedure. Blue boxes correspond to computational processes, red boxes represent the application of p-values cut-offs. The CIRC and the DOM period calculation procedures are two different modes that the original periodicity detection algorithm could operate [12] and correspond to two different ways to search for periods. CIRC performs an integer division of the genome length and DOM an exhaustive (by increments of 3 bps) fine comb of all potential periods within the user specified range. The process reports a table (available for downloading) of all the detected periods that is used downstream for plotting as a “periodobar”. Significant periods are directed to the second step of the analysis for the generation of “clustergram(s)”