Computational prediction of nucleosome positioning by calculating the relative fragment frequency index of nucleosomal sequences

Ryu Ogawa, Noriyuki Kitagawa, Hiroki Ashida, Rintaro Saito, Masaru Tomita

研究成果: Article

13 引用 (Scopus)

抄録

We developed an accurate method to predict nucleosome positioning from genome sequences by refining the previously developed method of Peckham et al. (2007) [19]. 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.

元の言語English
ページ(範囲)1498-1502
ページ数5
ジャーナルFEBS Letters
584
発行部数8
DOI
出版物ステータスPublished - 2010 4

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Nucleosomes
DNA sequences
Refining
Support vector machines
Genes
ROC Curve
Experiments
Genome

ASJC Scopus subject areas

  • Biochemistry
  • Biophysics
  • Cell Biology
  • Genetics
  • Molecular Biology
  • Structural Biology

これを引用

Computational prediction of nucleosome positioning by calculating the relative fragment frequency index of nucleosomal sequences. / Ogawa, Ryu; Kitagawa, Noriyuki; Ashida, Hiroki; Saito, Rintaro; Tomita, Masaru.

:: FEBS Letters, 巻 584, 番号 8, 04.2010, p. 1498-1502.

研究成果: Article

Ogawa, Ryu ; Kitagawa, Noriyuki ; Ashida, Hiroki ; Saito, Rintaro ; Tomita, Masaru. / Computational prediction of nucleosome positioning by calculating the relative fragment frequency index of nucleosomal sequences. :: FEBS Letters. 2010 ; 巻 584, 番号 8. pp. 1498-1502.
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