mosta

Overview Count Statistic Similarity Statistic Clustering Co-Occurrences

Calculate Co-Occurrences Reference

Calculate Similarity
Set of PFMs:	AC A5 XX TY Motif ID A BF undef P0 A C G T 01 18 7 26 9 02 9 13 5 33 03 32 13 6 9 04 14 28 9 9 05 10 9 28 13 06 4 8 9 39 XX // XX TY Motif ID B BF undef P0 A C G T 01 32 13 6 9 02 14 28 9 9 03 10 9 28 13 04 4 8 9 39 05 18 7 26 9 06 9 13 5 33 XX //	PFMs in transfac format. The program assumes the line tag ID to occur first. Next, it searches for P0, 01, 02 and so on until the next line does not contain the next number. End of PFM or separation between two PFMs has to be a line only containing two slashes '//'.
GC-content:		gc content, e.g. '.4', for the background model
threshold method:	typeI typeII balanced typeIext threshold	typeI: set threshold such that typeI error is equal to threshold-parameter. The typeI error is measured as the probability of at least one false positive in a region of length 500. typeII: set threshold such that typeII error is equal to threshold-parameter. balanced: set threshold such that typeI error equals typeII, threshold-parameter can be any number (is not used but has to be passed as parameter) typeIext: set threshold to balanced threshold and ensure that the typeI error for the next higher threshold is less than the threshold parameter. threshold: threshold-parameter contains the threshold.
threshold parameter		see threshold method.
window size		Size of the window for the co-occurrence probability.
		Download the exectuables to retrieve rates or to incorporate empirical occurrence probabilities.

© Utz J. Pape 2008