PERFECTOS-APE software predicts possible regulatory role of single nucleotide variants (SNVs) or polymorphisms (SNPs). The main idea is that SNVs may be located directly within transcription factor binding sites and different SNV alleles can change binding affinity.
PERFECTOS-APE efficiently tests SNVs against several collections of transcription factor binding site (TFBS) models represented as position weight matrices (PWM, PSSM).
Standalone command-line version (requires Java 1.6) is available for download (binary, sources). Current version is 3.0.3, please always use the latest version as previous versions may contain some bugs.
Program manual is available here.
Project page on github.
TFBS motif collections in the proper format can be downloaded here.