title: A novel alignment-free method for comparing transcription factor binding site motifs.
abstract: BACKGROUND
  Transcription factor binding site (TFBS) motifs can be accurately represented by position frequency matrices (PFM) or other equivalent forms. We often need to compare TFBS motifs using their PFMs in order to search for similar motifs in a motif database, or cluster motifs according to their binding preference. The majority of current methods for motif comparison involve a similarity metric for column-to-column comparison and a method to find the optimal position alignment between the two compared motifs. In some applications, alignment-free methods might be preferred; however, few such methods with high accuracy have been described.
  
  
  RESULTS
  Here we describe a novel alignment-free method for quantifying the similarity of motifs using their PFMs by converting PFMs into k-mer vectors. The motifs could then be compared by measuring the similarity among their corresponding k-mer vectors.
  
  
  CONCLUSIONS
  We demonstrate that our method in general achieves similar performance or outperforms the existing methods for clustering motifs according to their binding preference and identifying similar motifs of transcription factors of the same family.
authors.affiliation: Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte, North Carolina, United States of America.
authors.forename: Minli
authors.initials: M
authors.lastname: Xu
authors.forename: Zhengchang
authors.initials: Z
authors.lastname: Su
mesh_terms: D000465:Algorithms; D020816:Amino Acid Motifs; D001665:Binding Sites; D016000:Cluster Analysis; D014157:Transcription Factors / Q000737:chemistry / Q000378:metabolism*
chemical_list: D014157:Transcription Factors