- Communication -

Volume 6

Full article

MACO: A gapped-alignment scoring tool for comparing transcription factor binding sites

Gang Su, Binchen Mao and Jin Wang*

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


* Corresponding author
  Email: jwang@nju.edu.cn


Edited by E. Wingender; received May 17, 2006; revised and accepted May 23, 2006; published May 29, 2006

Abstract

We have implemented a novel gapped-alignment algorithm to compare Position Frequency Matrices (PFM) 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 Matrices (PFM), gap, alignment, transcription factor binding site (TFBS)