GPU Based Composite Elements Discovery in Large DNADatasets

Oleg Vishnevsky, Andrey Bocharnikov, Nikolay Kolchanov

Research output: Chapter in Book/Report/Conference proceedingConference contributionResearchpeer-review

Abstract

Composite elements play an important role in the regulation of transcription. Existing methods for the revealing of potential composite elements are usually based on assessment of the significance of the mutual presence of the predicted transcription factor binding sites using weight matrices or other methods trained on samples of binding sites of known transcription factors. Thus, such methods essentially depend on the completeness of training samples and information on existing TFs. We have proposed a method for de novo discovery of potential composite elements, which does not require preliminary information about the localization of potential TFBS. Using the proposed approach, context signals are identified in the ChIP-Seq dataset, which can correspond to potential composite elements.

Original languageEnglish
Title of host publicationProceedings - 2020 Cognitive Sciences, Genomics and Bioinformatics, CSGB 2020
PublisherInstitute of Electrical and Electronics Engineers Inc.
Pages135-138
Number of pages4
ISBN (Electronic)9781728195971
DOIs
Publication statusPublished - Jul 2020
Event2020 Cognitive Sciences, Genomics and Bioinformatics, CSGB 2020 - Novosibirsk, Russian Federation
Duration: 6 Jul 202010 Jul 2020

Publication series

NameProceedings - 2020 Cognitive Sciences, Genomics and Bioinformatics, CSGB 2020

Conference

Conference2020 Cognitive Sciences, Genomics and Bioinformatics, CSGB 2020
CountryRussian Federation
CityNovosibirsk
Period06.07.202010.07.2020

Keywords

  • ChIP-Seq
  • composite elements
  • oligonucleotide motifs
  • transcription regulation

OECD FOS+WOS

  • 1.02 COMPUTER AND INFORMATION SCIENCES
  • 1.06 BIOLOGICAL SCIENCES
  • 3.01 BASIC MEDICAL RESEARCH
  • 3.03 HEALTH SCIENCES
  • 5.09 OTHER SOCIAL SCIENCES

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