title: Computational prediction of nucleosome positioning by calculating the relative fragment frequency index of nucleosomal sequences.
abstract: We developed an accurate method to predict nucleosome positioning from genome sequences by refining the previously developed method of Peckham et al. (2007). Here, we used the relative fragment frequency index we developed and a support vector machine to screen for nucleosomal and linker DNA sequences. Our twofold cross-validation revealed that the accuracy of our method based on the area under the receiver operating characteristic curve was 81%, whereas that of Peckham's method was 75% when both of two nucleosomal sequence data obtained from independent experiments were used for validation. We suggest that our method is more effective in predicting nucleosome positioning.
authors.affiliation: Institute for Advanced Biosciences, Keio University, Tsuruoka, Japan.
authors.forename: Ryu
authors.initials: R
authors.lastname: Ogawa
authors.forename: Noriyuki
authors.initials: N
authors.lastname: Kitagawa
authors.forename: Hiroki
authors.initials: H
authors.lastname: Ashida
authors.forename: Rintaro
authors.initials: R
authors.lastname: Saito
authors.forename: Masaru
authors.initials: M
authors.lastname: Tomita
mesh_terms: D019540:Area Under Curve; D001185:Artificial Intelligence; D001483:Base Sequence; D047369:Chromatin Immunoprecipitation; D003198:Computer Simulation; D004247:DNA / Q000235:genetics; D023281:Genomics; D008954:Models, Biological; D009707:Nucleosomes / Q000235:genetics*; D012372:ROC Curve; D015203:Reproducibility of Results; D012441:Saccharomyces cerevisiae / Q000235:genetics
chemical_list: D009707:Nucleosomes; D004247:DNA