title: MACO: a gapped-alignment scoring tool for comparing transcription factor binding sites.
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 authors.
authors.affiliation: The State Key Laboratory of Pharmaceutical Biotechnology and Model Animal Institute, Department of Biochemistry, Nanjing University, Nanjing 210093, PR China.
authors.forename: Gang
authors.initials: G
authors.lastname: Su
authors.forename: Binchen
authors.initials: B
authors.lastname: Mao
authors.forename: Jin
authors.initials: J
authors.lastname: Wang
mesh_terms: D000465:Algorithms; D001483:Base Sequence; D001665:Binding Sites; D004247:DNA / Q000235:genetics / Q000378:metabolism; D011485:Protein Binding; D014157:Transcription Factors / Q000378:metabolism*
chemical_list: D014157:Transcription Factors; D004247:DNA