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PXD038899

PXD038899 is an original dataset announced via ProteomeXchange.

Dataset Summary
TitleSnapper: a high-sensitive algorithm to detect methylation motifs based on Oxford Nanopore reads
DescriptionThe Oxford Nanopore technology has a great potential for the analysis of genome methylation, including full-genome methylome profiling. However, there are certain issues while identifying methylation motif sequences caused by low sensitivity of the currently available motif enrichment algorithms. Here, we present Snapper, a new highly-sensitive approach to extract methylation motif sequences based on a greedy motif selection algorithm. Snapper has shown higher enrichment sensitivity compared with the MEME tool coupled with Tombo or Nanodisco instruments, which was demonstrated on H. pylori strain J99 studied earlier using the PacBio technology. In addition, we used Snapper to characterize the total methylome of a new H.pylori strain A45. The analysis revealed the presence of at least 4 methylation sites that have not been described for H. pylori earlier. We experimentally confirmed a new CCAG-specific methyltransferase and indirectly inferred a new CCAAK-specific methyltransferase.
HostingRepositoryPRIDE
AnnounceDate2024-10-22
AnnouncementXMLSubmission_2024-10-22_06:27:52.903.xml
DigitalObjectIdentifier
ReviewLevelPeer-reviewed dataset
DatasetOriginOriginal dataset
RepositorySupportUnsupported dataset by repository
PrimarySubmitterIvan Butenko
SpeciesList scientific name: Helicobacter pylori J99 (Campylobacter pylori J99); NCBI TaxID: 85963;
ModificationListNo PTMs are included in the dataset
InstrumentQ Exactive HF-X
Dataset History
RevisionDatetimeStatusChangeLog Entry
02022-12-19 02:55:31ID requested
12024-01-26 14:20:27announced
22024-10-22 06:27:53announced2024-10-22: Updated project metadata.
Publication List
10.1093/bioinformatics/btad702;
Konanov DN, Babenko VV, Belova AM, Madan AG, Boldyreva DI, Glushenko OE, Butenko IO, Fedorov DE, Manolov AI, Krivonos DV, Lazarev VN, Govorun VM, Ilina EN, Snapper: high-sensitive detection of methylation motifs based on Oxford Nanopore reads. Bioinformatics, 39(11):(2023) [pubmed]
Keyword List
submitter keyword: methylation,Helicobacter pylori, strain
Contact List
Ivan Butenko
contact affiliationSRI for Systems Biology and Medicine
contact emailivan.butenko@sysbiomed.ru
lab head
Ivan Butenko
contact affiliationScientific Research Institute for Systems Biology and Medicine, Moscow, Russian Federation
contact emailivan.butenko@gmail.com
dataset submitter
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Dataset FTP location
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