title: NCS: incorporating positioning data to quantify nucleosome stability in yeast.
abstract: BACKGROUND
  With the spreading technique of mass sequencing, nucleosome positions and scores for their intensity have become available through several previous studies in yeast, but relatively few studies have specifically aimed to determine the score of nucleosome stability. Based on mass sequencing data, we proposed a nucleosome center score (NCS) for quantifying nucleosome stability by measuring shifts of the nucleosome center, and then mapping NCS scores to nucleosome positions in Brogaard et al.'s study.
  
  
  RESULTS
  We demonstrated the efficiency of NCS by known preference of A/T-based tracts for nucleosome formation, and showed that central nucleosomal DNA is more sensitive to A/T-based tracts than outer regions, which corresponds to the central histone tetramer-dominated region. We also found significant flanking preference around nucleosomal DNA for A/T-based dinucleotides, suggesting that neighboring sequences could affect nucleosome stability. Finally, the difference between results of NCS and Brogaard et al.'s scores was addressed and discussed.
  
  
  BACKGROUND
  jchiang@mail.ncku.edu.tw
  
  
  BACKGROUND
  Supplementary data are available at Bioinformatics online.
authors.affiliation: Department of Computer Science and Information Engineering, National Cheng Kung University, Tainan 70101, Taiwan.
authors.forename: Jung-Hsien
authors.initials: JH
authors.lastname: Chiang
authors.forename: Chan-Hsien
authors.initials: CH
authors.lastname: Lin
mesh_terms: D004271:DNA, Fungal / Q000235:genetics; D059014:High-Throughput Nucleotide Sequencing; D009707:Nucleosomes / Q000235:genetics*; D011061:Poly A / Q000235:genetics; D011071:Poly T / Q000235:genetics; D012441:Saccharomyces cerevisiae / Q000235:genetics* / Q000378:metabolism
chemical_list: D004271:DNA, Fungal; D009707:Nucleosomes; D011061:Poly A; D011071:Poly T