Database Commons

a catalog of biological databases

e.g., animal; RNA; Methylation; China

Database Profile

General information

URL: http://sysbio.sysu.edu.cn/methsmrt/
Full name:
Description: An integrative database for DNA 6mA and 4mC methylomes, generated from SMRT sequencing. The database provides a platform to host, browse, search and download 6mA and 4mC profiles for 156 species. It also offers a genome browser to visualize DNA methylation sites and related information such as SNPs and gene annotation.
Year founded: 2016
Last update: 2016-07-28
Version:
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Country/Region: China
Data type:
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Contact information

University/Institution: Sun Yat-sen University
Address: No. 54, XianlieNan Road, Yuexiu District
City: Guangzhou
Province/State: Guangdong
Country/Region: China
Contact name (PI/Team): Zhi Xie
Contact email (PI/Helpdesk): xiezhi@gmail.com

Publications

27924023
MethSMRT: an integrative database for DNA N6-methyladenine and N4-methylcytosine generated by single-molecular real-time sequencing. [PMID: 27924023]
Ye P, Luan Y, Chen K, Liu Y, Xiao C, Xie Z.

DNA methylation is an important type of epigenetic modifications, where 5- methylcytosine (5mC), 6-methyadenine (6mA) and 4-methylcytosine (4mC) are the most common types. Previous efforts have been largely focused on 5mC, providing invaluable insights into epigenetic regulation through DNA methylation. Recently developed single-molecule real-time (SMRT) sequencing technology provides a unique opportunity to detect the less studied DNA 6mA and 4mC modifications at single-nucleotide resolution. With a rapidly increased amount of SMRT sequencing data generated, there is an emerging demand to systematically explore DNA 6mA and 4mC modifications from these data sets. MethSMRT is the first resource hosting DNA 6mA and 4mC methylomes. All the data sets were processed using the same analysis pipeline with the same quality control. The current version of the database provides a platform to store, browse, search and download epigenome-wide methylation profiles of 156 species, including seven eukaryotes such as Arabidopsis, C. elegans, Drosophila, mouse and yeast, as well as 149 prokaryotes. It also offers a genome browser to visualize the methylation sites and related information such as single nucleotide polymorphisms (SNP) and genomic annotation. Furthermore, the database provides a quick summary of statistics of methylome of 6mA and 4mC and predicted methylation motifs for each species. MethSMRT is publicly available at http://sysbio.sysu.edu.cn/methsmrt/ without use restriction. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

Nucleic Acids Res. 2017:45(D1) | 32 Citations (from Europe PMC, 2021-06-19)

Ranking

All databases:
1015/5061 (79.964%)
Modification:
50/228 (78.509%)
Genotype phenotype and variation:
138/705 (80.567%)
1015
Total Rank
32
Citations
8
z-index

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Record metadata

Created on: 2017-02-13
Curated by:
Shixiang Sun [2017-02-13]