TFBS Scanner provides command line software toolsets for two useful types of TFBS (Transcription Factor Binding Site) Scanning using Positional Weight Matrices (PWMs):
The Scanner Toolset
Scanning with a fixed background model (can be toggled to 0th order or 1st order Markov, currently set as 1st order), with PWM-specific thresholds generated using this same background
The SpeakerScan Toolset
Scanning with a local background correction, outputs log-likelihood scores which can then be post-processed as desired
:: MORE INFORMATION
Morton T, Petricka J, Corcoran DL, Li S, Winter CM, Carda A, Benfey PN, Ohler U, Megraw M. (2014).
Paired-end analysis of transcription start sites in Arabidopsis reveals plant-specific promoter signatures.
Plant Cell, 26:2746-60.
Megraw M, Pereira F, Jensen ST, Ohler U, Hatzigeorgiou AG. (2009).
A transcription factor affinity based code for mammalian transcription initiation.
Genome Research, 19:644-56.