2. FAQ

Frequently Asked Questions

1. How do I cite the ASMdb?

2. How to calculate the sulfite conversion of data?

3. How does the database collect and download data?

4. Why are some samples missing from the genome browser?

5. What is the definition of promoter?

6. What is the range of DNA methylation levels in ASMdb?

If you have any questions, please contact us in time.


1. How do I cite the ASMdb? Back to top

Zhou Q, Guan P, Zhu Z, Cheng S, Zhou C, Wang H, Xu Q, Sung WK, Li G. ASMdb: a comprehensive database for allele-specific DNA methylation in diverse organisms. Nucleic Acids Res. 2021 Oct 19:gkab937. doi: 10.1093/nar/gkab937. PMID: 34664666.

2. How to calculate the sulfite conversion of data ? Back to top

Human and mouse were evaluated for sulfite conversion by calculating CHG methylation, while Arabidopsis was evaluated by calculating chloroplast methylation.

3. How does the database collect and download data ? Back to top

We conducted a total of 3 times data collections on GEO, the search details as follows: 1) The first phase. Search term: WGBS OR BS-Seq Publication date: to 2019/01/15 Search details: WGBS [All Fields] OR BS-Seq [All Fields] AND ("0001/01/01"[PDAT] : "2019/01/15"[PDAT])

2) The second phase. Search term: WGBS OR BS-Seq OR Bisulfite-Seq OR "Bisulfite sequencing" OR WGBS-Seq Publication date: to 2019/09/20 Search details: WGBS [All Fields] OR BS-Seq [All Fields] OR Bisulfite-Seq [All Fields] OR "Bisulfite sequencing"[All Fields] OR WGBS-Seq [All Fields] AND ("gse"[Filter] AND ("0001/01/01"[PDAT]: "2019/09/20"[PDAT]))

3) The third phase. Search term: MethylC-Seq Publication date: to 2019/09/20 Search details: MethylC-Seq[All Fields] AND ("0001/01/01"[PDAT] : "2019/09/20"[PDAT]) We deleted duplicate data and removed the data not public in NCBI. Besides, we removed low quality data through bisulfite conversion and coverage.

4. Why are some samples missing from the genome browser? Back to top

We excluded the lower coverage (< 5x) and low quality BS-Seq data.

5. What is the definition of promoter? Back to top

We defined the 2K region upstream of the transcription start position (TSS) as the promoter.

6. What is the range of DNA methylation levels in ASMdb? Back to top

DNA methylation levels range from 0 to 1 in ASMdb.