I wonder if you could kindly point me to a clear description of the algorithm that matchPWM implementation is based on, preferably a peer-reviewed publication.
I apologize in advance for not being able to see the obvious answer here. But the reference (Wasserman and Sandelin, 2004 Nat. Gen. Rev.) in the matchPWM documentation seems to serve only a general concept of PWM function itself rather than the matchPWM.
The closest paper I could find is MATCH in NAR. Am I correct assume it is the same algorithm for matchPWM?
1. Wasserman, W. W. & Sandelin, A. Applied bioinformatics for the identification of regulatory elements. Nat Rev Genet 5, 276–287 (2004).
2. Kel, A. E. MATCHTM: a tool for searching transcription factor binding sites in DNA sequences. Nucleic Acids Res 31, 3576–3579 (2003).