Abstract: We have implemented a novel gapped-alignment algorithm to compare
Position Frequency Matrices (PFMs) for Transcription Factor Binding Sites. The
application compares an input PFM with those collected from public databases
and outputs similarity scores, sequence alignments and related PFM clusters.
MACO is freely accessible on a web server located at
www.nicemice.cn/bioinfo/MACO. Source code is distributed upon request to the
Keywords: Position Frequency Matrix (PFM), gap, alignment, transcription factor binding site (TFBS)