PXD038899

PXD038899 is an original dataset announced via ProteomeXchange.

Title	Snapper: a high-sensitive algorithm to detect methylation motifs based on Oxford Nanopore reads
Description	The 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.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_06:27:52.903.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Ivan Butenko
SpeciesList	scientific name: Helicobacter pylori J99 (Campylobacter pylori J99); NCBI TaxID: 85963;
ModificationList	No PTMs are included in the dataset
Instrument	Q Exactive HF-X

Revision	Datetime	Status	ChangeLog Entry
0	2022-12-19 02:55:31	ID requested
1	2024-01-26 14:20:27	announced
⏵ 2	2024-10-22 06:27:53	announced	2024-10-22: Updated project metadata.

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]

submitter keyword: methylation,Helicobacter pylori, strain

Ivan Butenko
contact affiliation	SRI for Systems Biology and Medicine
contact email	ivan.butenko@sysbiomed.ru
lab head
Ivan Butenko
contact affiliation	Scientific Research Institute for Systems Biology and Medicine, Moscow, Russian Federation
contact email	ivan.butenko@gmail.com
dataset submitter

Dataset FTP location NOTE: Most web browsers have now discontinued native support for FTP access within the browser window. But you can usually install another FTP app (we recommend FileZilla) and configure your browser to launch the external application when you click on this FTP link. Or otherwise, launch an app that supports FTP (like FileZilla) and use this address: ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2024/01/PXD038899

PRIDE project URI

• PRIDE
  1. PXD038899
     1. Label: PRIDE project
     2. Name: Snapper: a high-sensitive algorithm to detect methylation motifs based on Oxford Nanopore reads