PXD038899 is an
original dataset announced via ProteomeXchange.
Dataset Summary
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 |
Dataset History
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. |
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 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 | |
Full Dataset Link List
Dataset FTP location
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PRIDE project URI |
Repository Record List
[ + ]
[ - ]
- PRIDE
- PXD038899
- Label: PRIDE project
- Name: Snapper: a high-sensitive algorithm to detect methylation motifs based on Oxford Nanopore reads