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Identifying centromeric satellites with dna-brnn.

ABSTRACT: SUMMARY:Human alpha satellite and satellite 2/3 contribute to several percent of the human genome. However, identifying these sequences with traditional algorithms is computationally intensive. Here we develop dna-brnn, a recurrent neural network to learn the sequences of the two classes of centromeric repeats. It achieves high similarity to RepeatMasker and is times faster. Dna-brnn explores a novel application of deep learning and may accelerate the study of the evolution of the two repeat classes. AVAILABILITY AND IMPLEMENTATION:https://github.com/lh3/dna-nn.

SUBMITTER: Li H

PROVIDER: S-EPMC6821349 | biostudies-literature | 2019 Nov

REPOSITORIES: biostudies-literature

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Identifying centromeric satellites with dna-brnn.

Li Heng H

Bioinformatics (Oxford, England) 20191101 21

<h4>Summary</h4>Human alpha satellite and satellite 2/3 contribute to several percent of the human genome. However, identifying these sequences with traditional algorithms is computationally intensive. Here we develop dna-brnn, a recurrent neural network to learn the sequences of the two classes of centromeric repeats. It achieves high similarity to RepeatMasker and is times faster. Dna-brnn explores a novel application of deep learning and may accelerate the study of the evolution of the two re ...[more]

PMID: 30989183

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