MACRO-PERFECTOS-APE — MAtrix CompaRisOn & PrEdicting Regulatory Functional Effect of SNPs by Approximate P-value Estimation

Here we present MACRO-APE and PERFECTOS-APE software designed for practical sequence analysis involving classic mononucleotide and dinucleotide position weight matrices (PWMs) of DNA sequence patterns often called motifs. The common usage case for DNA motifs is representation of transcription factor binding sites. The software allows (1) comparing different PWMs using a variant of Jaccard similarity measure, e.g. scanning a motif collection for motifs similar to a given query, (2) analysing single-nucleotide variants for possible regulatory effect through transcription factor affinity changes, (3) performing basic PWM analysis (P-value and threshold estimation).