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Computational prediction of nucleosome positioning by calculating the relative fragment frequency index of nucleosomal sequences
Author(s) -
Ogawa Ryu,
Kitagawa Noriyuki,
Ashida Hiroki,
Saito Rintaro,
Tomita Masaru
Publication year - 2010
Publication title -
febs letters
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.593
H-Index - 257
eISSN - 1873-3468
pISSN - 0014-5793
DOI - 10.1016/j.febslet.2010.02.067
Subject(s) - nucleosome , fragment (logic) , linker dna , computational biology , dna sequencing , computer science , index (typography) , sequence (biology) , algorithm , dna , biology , genetics , histone , world wide web
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.