title: ChIPseqR: analysis of ChIP-seq experiments.
abstract: BACKGROUND
  The use of high-throughput sequencing in combination with chromatin immunoprecipitation (ChIP-seq) has enabled the study of genome-wide protein binding at high resolution. While the amount of data generated from such experiments is steadily increasing, the methods available for their analysis remain limited. Although several algorithms for the analysis of ChIP-seq data have been published they focus almost exclusively on transcription factor studies and are usually not well suited for the analysis of other types of experiments.
  
  
  RESULTS
  Here we present ChIPseqR, an algorithm for the analysis of nucleosome positioning and histone modification ChIP-seq experiments. The performance of this novel method is studied on short read sequencing data of Arabidopsis thaliana mononucleosomes as well as on simulated data.
  
  
  CONCLUSIONS
  ChIPseqR is shown to improve sensitivity and spatial resolution over existing methods while maintaining high specificity. Further analysis of predicted nucleosomes reveals characteristic patterns in nucleosome sequences and placement.
authors.affiliation: Department of Statistics, Macquarie University, North Ryde, NSW 2109, Australia. peter.humburg@well.ox.ac.uk
authors.forename: Peter
authors.initials: P
authors.lastname: Humburg
authors.forename: Chris A
authors.initials: CA
authors.lastname: Helliwell
authors.forename: David
authors.initials: D
authors.lastname: Bulger
authors.forename: Glenn
authors.initials: G
authors.lastname: Stone
mesh_terms: D000465:Algorithms; D017360:Arabidopsis / Q000235:genetics; D029681:Arabidopsis Proteins / Q000235:genetics; D001665:Binding Sites; D047369:Chromatin Immunoprecipitation / Q000379:methods*; D019295:Computational Biology / Q000379:methods; D018744:DNA, Plant / Q000235:genetics; D018745:Genome, Plant; D006657:Histones / Q000235:genetics; D015233:Models, Statistical; D009707:Nucleosomes / Q000235:genetics*; D012680:Sensitivity and Specificity; D017422:Sequence Analysis, DNA / Q000379:methods
chemical_list: D029681:Arabidopsis Proteins; D018744:DNA, Plant; D006657:Histones; D009707:Nucleosomes