Most analyses were performed in the GNU R environment (https://www.r-project.org, ver. 3.6.1). R packages were obtained from CRAN (https://cran.r-project.org/) and Bioconductor (http://bioconductor.org/). Chemical maps for budding yeast, fission yeast, and house mouse (Mus musculus) embryonic stem cells [17, 19, 22] were used for model construction and testing the prediction accuracy. The budding yeast's chemical map in the sacCer2 coordinate was lifted over to the sacCer3 coordinate, as described elsewhere [24]. The number of unique and redundant nucleosomes in the budding yeast genome was 67,548 and 344,709, respectively; fission yeast, 75,828 and 425,653; mice, 10,677,016 and 850,701,275. Reference genomes of budding yeast (R64-1-1), fission yeast (ASM294v2), and mice (mm9/NCBIM37.67) were used. The original 282-bp Widom 601 sequence [10], the 485-bp MMTV 3′-LTR sequence [53] and the somatic 5S RNA gene of Xenopus borealis [54] were used as test sequences.

Note: The content above has been extracted from a research article, so it may not display correctly.



Q&A
Please log in to submit your questions online.
Your question will be posted on the Bio-101 website. We will send your questions to the authors of this protocol and Bio-protocol community members who are experienced with this method. you will be informed using the email address associated with your Bio-protocol account.



We use cookies on this site to enhance your user experience. By using our website, you are agreeing to allow the storage of cookies on your computer.