Chemical map-based prediction of nucleosome positioning using the Bioconductor package nuCpos
نویسندگان
چکیده
منابع مشابه
PING 2.0: an R/Bioconductor package for nucleosome positioning using next-generation sequencing data
SUMMARY MNase-Seq and ChIP-Seq have evolved as popular techniques to study chromatin and histone modification. Although many tools have been developed to identify enriched regions, software tools for nucleosome positioning are still limited. We introduce a flexible and powerful open-source R package, PING 2.0, for nucleosome positioning using MNase-Seq data or MNase- or sonicated- ChIP-Seq data...
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BACKGROUND The DNA of all eukaryotic organisms is packaged into nucleosomes, the basic repeating units of chromatin. The nucleosome consists of a histone octamer around which a DNA core is wrapped and the linker histone H1, which is associated with linker DNA. By altering the accessibility of DNA sequences, the nucleosome has profound effects on all DNA-dependent processes. Understanding the fa...
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Using a recently developed chemical approach, we have generated a genome-wide map of nucleosomes in vivo in Schizosaccharomyces pombe (S. pombe) at base pair resolution. The shorter linker length previously identified in S. pombe is due to a preponderance of nucleosomes separated by ∼4/5 bp, placing nucleosomes on opposite faces of the DNA. The periodic dinucleotide feature thought to position ...
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We will briefly describe the second and third of these different aspects and then for the remainder of this vignette concentrate on the first category. The other three have their own vignettes. There are two different, but complementary strategies for accessing metadata. One is to use highly curated data that have been assembled from many different sources and a second is to rely on on-line sou...
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ژورنال
عنوان ژورنال: BMC Bioinformatics
سال: 2021
ISSN: 1471-2105
DOI: 10.1186/s12859-021-04240-2