MACRO-APE software allows efficient comparison of transcription factor binding models (often called motifs) represented as position weight matrices (PWMs, also known as Position Specific Scoring Matrices, PSSMs) with score thresholds.
Online interface is available here.
Standalone command-line version (requires Java 1.6) is available for download (binary, sources). Current version is 2.0.3, please always use the latest version as previous versions may contain some bugs.
Standalone version in ruby (a bit obsolete and slower) is available here.
The program manual for ruby version is available here.
Program manual is available here.
Project page on github.
TFBS motif collections in the proper format can be downloaded here.