title: An alignment-free model for comparison of regulatory sequences.
abstract: BACKGROUND
  Some recent comparative studies have revealed that regulatory regions can retain function over large evolutionary distances, even though the DNA sequences are divergent and difficult to align. It is also known that such enhancers can drive very similar expression patterns. This poses a challenge for the in silico detection of biologically related sequences, as they can only be discovered using alignment-free methods.
  
  
  RESULTS
  Here, we present a new computational framework called Regulatory Region Scoring (RRS) model for the detection of functional conservation of regulatory sequences using predicted occupancy levels of transcription factors of interest. We demonstrate that our model can detect the functional and/or evolutionary links between some non-alignable enhancers with a strong statistical significance. We also identify groups of enhancers that are likely to be similarly regulated. Our model is motivated by previous work on prediction of expression patterns and it can capture similarity by strong binding sites, weak binding sites and even the statistically significant absence of sites. Our results support the hypothesis that weak binding sites contribute to the functional similarity of sequences. Our model fills a gap between two families of models: detailed, data-intensive models for the prediction of precise spatio-temporal expression patterns on the one side, and crude, generally applicable models on the other side. Our model borrows some of the strengths of each group and addresses their drawbacks.
  
  
  BACKGROUND
  The RRS source code is freely available upon publication of this manuscript: http://www2.warwick.ac.uk/fac/sci/systemsbiology/staff/ott/tools_and_software/rrs.
authors.affiliation: MOAC Doctoral Training Centre, Coventry House, University of Warwick, Coventry, CV4 7AL, UK. hashem.koohy@warwick.ac.uk
authors.forename: Hashem
authors.initials: H
authors.lastname: Koohy
authors.forename: Nigel P
authors.initials: NP
authors.lastname: Dyer
authors.forename: John E
authors.initials: JE
authors.lastname: Reid
authors.forename: Georgy
authors.initials: G
authors.lastname: Koentges
authors.forename: Sascha
authors.initials: S
authors.lastname: Ott
mesh_terms: D000465:Algorithms; D001483:Base Sequence; D001665:Binding Sites; D004247:DNA / Q000737:chemistry*; D030541:Databases, Genetic; D012045:Regulatory Sequences, Nucleic Acid / Q000235:genetics*; D016415:Sequence Alignment / Q000379:methods*; D017422:Sequence Analysis, DNA / Q000379:methods*
chemical_list: D004247:DNA