MACO: A Gapped-Alignment Scoring Tool for Comparing Transcription Factor Binding Sites

Article type: Research Article

Authors: Su, Gang | Mao, Binchen | Wang, Jin

Affiliations: The State Key Laboratory of Pharmaceutical Biotechnology and Model Animal Institute, Department of Biochemistry, Nanjing University, Nanjing 210093, P.R. China

Note: [] Corresponding author. E-mail: [email protected]

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.

Keywords: Position Frequency Matrix (PFM), gap, alignment, transcription factor binding site (TFBS)

Journal: In Silico Biology, vol. 6, no. 4, pp. 307-310, 2006