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Universal correction of enzymatic sequence bias reveals molecular signatures of protein/DNA interactions.


ABSTRACT: Coupling molecular biology to high-throughput sequencing has revolutionized the study of biology. Molecular genomics techniques are continually refined to provide higher resolution mapping of nucleic acid interactions and structure. Sequence preferences of enzymes can interfere with the accurate interpretation of these data. We developed seqOutBias to characterize enzymatic sequence bias from experimental data and scale individual sequence reads to correct intrinsic enzymatic sequence biases. SeqOutBias efficiently corrects DNase-seq, TACh-seq, ATAC-seq, MNase-seq and PRO-seq data. We show that seqOutBias correction facilitates identification of true molecular signatures resulting from transcription factors and RNA polymerase interacting with DNA.

SUBMITTER: Martins AL 

PROVIDER: S-EPMC5778497 | biostudies-literature | 2018 Jan

REPOSITORIES: biostudies-literature

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Universal correction of enzymatic sequence bias reveals molecular signatures of protein/DNA interactions.

Martins André L AL   Walavalkar Ninad M NM   Anderson Warren D WD   Zang Chongzhi C   Guertin Michael J MJ  

Nucleic acids research 20180101 2


Coupling molecular biology to high-throughput sequencing has revolutionized the study of biology. Molecular genomics techniques are continually refined to provide higher resolution mapping of nucleic acid interactions and structure. Sequence preferences of enzymes can interfere with the accurate interpretation of these data. We developed seqOutBias to characterize enzymatic sequence bias from experimental data and scale individual sequence reads to correct intrinsic enzymatic sequence biases. Se  ...[more]

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