Algorithmic Issues in the Analysis of Chip‐Seq Data

Zambelli, Federico; Pavesi, Giulio

doi:10.1002/9780470892107.ch20

Cited by 1 publication

(2 citation statements)

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“…As shown in Figure 1 , a nucleosome is composed of a DNA sequence wrapped 1.65 times around a histone octamer [ 3 ]. If the DNA region is wrapped compactly to prevent proteins from binding to the DNA, the corresponding gene is not transcribed [ 4 ]. Therefore, nucleosomes can regulate gene expression by restricting or facilitating the DNA accessibility of proteins.…”

Section: Introductionmentioning

confidence: 99%

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NucVoter: A Voting Algorithm for Reliable Nucleosome Prediction Using Next-Generation Sequencing Data

Byeon

2013

ISRN Bioinformatics

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Nucleosomes, which consist of DNA wrapped around histone octamers, are dynamic, and their structure, including their location, size, and occupancy, can be transformed. Nucleosomes can regulate gene expression by controlling the DNA accessibility of proteins. Using next-generation sequencing techniques along with such laboratory methods as micrococcal nuclease digestion, predicting the genomic locations of nucleosomes is possible. However, the true locations of nucleosomes are unknown, and it is difficult to determine their exact locations using next-generation sequencing data. This paper proposes a novel voting algorithm, NucVoter, for the reliable prediction of nucleosome locations. Multiple models verify the consensus areas in which nucleosomes are placed by the model with the highest priority. NucVoter significantly improves the performance of nucleosome prediction.

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Section: Introductionmentioning

confidence: 99%

“…Nucleosome prediction refers to nucleosome positioning in the genome. Using MNase-seq or Chip-seq, it is possible to identify the genomic locations of nucleosomes [ 4 , 5 , 8 ]. Micrococcal nuclease (MNase) is a restriction enzyme that digests DNA that is not wrapped around histones.…”

Section: Introductionmentioning

confidence: 99%

NucVoter: A Voting Algorithm for Reliable Nucleosome Prediction Using Next-Generation Sequencing Data

Byeon

2013

ISRN Bioinformatics

View full text Add to dashboard Cite

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Algorithmic Issues in the Analysis of Chip‐Seq Data

Cited by 1 publication

References 61 publications

NucVoter: A Voting Algorithm for Reliable Nucleosome Prediction Using Next-Generation Sequencing Data

NucVoter: A Voting Algorithm for Reliable Nucleosome Prediction Using Next-Generation Sequencing Data

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