Draft:MethPrimer
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| MethPrimer | |
|---|---|
| Developer(s) | Long-Cheng Li |
| Initial release | November 2002 |
| Operating system | Web-based (cross-platform) |
| Type | Bioinformatics |
| License | Freeware |
| Website | methprimer |
MethPrimer is a free, web-based program for designing primers used in PCR-based analysis of DNA methylation. It is specifically designed to work with bisulfite-converted DNA, a common technique in epigenetics research. MethPrimer supports the design of primers for methylation-specific PCR (MSP) and bisulfite sequencing PCR (BSP). It also includes a feature for predicting CpG islands. The program was created by Dr. Long-Cheng Li and is currently maintained by Ractigen Therapeutics, a biotechnology company founded by Dr. Li in 2017.
History
[edit]MethPrimer was developed by Dr. Long-Cheng Li in 2002 while he was a research scientist at the University of California, San Francisco (UCSF). The program was created to address the growing need for a specialized tool to design primers for bisulfite-based methylation studies, a technique that was becoming increasingly important in epigenetics research. The original MethPrimer program was described in a Bioinformatics journal article published in 2002.[1] The program was originally hosted on the UCSF Li Lab website and was later moved to its own domain, methprimer.com, and is maintained by Ractigen Therapeutics.
Features
[edit]MethPrimer offers several key features for methylation analysis:
- Methylation-Specific PCR (MSP) Primer Design: MethPrimer designs two pairs of primers for MSP: one pair specific to methylated DNA and another pair specific to unmethylated DNA. This allows researchers to determine the methylation status of a specific DNA region.
- Bisulfite Sequencing PCR (BSP) Primer Design: MethPrimer designs primers that amplify bisulfite-converted DNA without bias towards methylated or unmethylated sequences. These primers are used for sequencing-based methylation analysis, providing a detailed view of methylation patterns.
- CpG Island Prediction: MethPrimer can predict CpG islands within a given DNA sequence. CpG islands are regions with a high frequency of CpG dinucleotides, often associated with gene promoters and regulatory elements. The prediction is based on parameters such as GC content, observed/expected CpG ratio, and window size.
- Input Flexibility: Users can input DNA sequences in various standard formats. The program handles the bisulfite conversion simulation internally, so users do not need to pre-edit their sequences.
- Output Formats: MethPrimer provides results in both text and graphical formats, making it easy to visualize primer locations and CpG island predictions.
Algorithm
[edit]MethPrimer's primer design process involves several steps:
1. Bisulfite Conversion Simulation: The input DNA sequence is computationally "converted" to simulate the effects of bisulfite treatment. Non-CpG cytosines are changed to thymines. For MSP, both a fully converted sequence (representing unmethylated DNA) and a sequence where all cytosines are protected (representing methylated DNA) are generated. 2. Oligo Testing: All possible short oligonucleotide sequences (potential primers) within the converted sequence(s) are evaluated based on various parameters, including:
- GC content
- Melting temperature (Tm)
- Number of non-CpG cytosines
- Presence and location of CpGs (for MSP primers)
- Maximum number of consecutive mononucleotides (Poly X and Poly T rules)
3. Primer Pair Matching: Potential upstream and downstream primers are paired and evaluated based on:
- Product size
- Melting temperature difference between primers (especially for MSP)
- Location relative to the target region and predicted CpG islands
4. Parameter Filtering: Primer pairs are filtered based on user-defined constraints, such as product size range, primer size range, Tm range, and specific requirements for BSP and MSP primers.
5. Output: The program returns a list of primer pairs that best meet the specified criteria.
Impact and usage
[edit]MethPrimer has been widely used in the scientific community and has been cited in over 2,900 peer-reviewed publications as of 2025. It is considered a standard tool in the field of epigenetics research, particularly for studies involving DNA methylation. The program's longevity and continued use demonstrate its utility and reliability.
See also
[edit]- Bioinformatics
- Bisulfite sequencing
- CpG island
- DNA methylation
- Methylation-specific PCR
- Polymerase chain reaction
- Primer (molecular biology)
References
[edit]- Widespread academic use and citation: The original MethPrimer paper has been cited over 3,000 times in peer-reviewed scientific journals. This high number of citations indicates its importance and widespread adoption as a key tool in its field. You can view the citations on Google Scholar: https://scholar.google.com/scholar?oi=bibs&hl=en&cites=237274526441137866&as_sdt=5.
- Inclusion in university resources: MethPrimer is included in the software and database collections of numerous universities and research institutions worldwide, indicating its value in an academic setting. Here are a few examples:
- https://www.hsls.pitt.edu/obrc/index.php?page=URL1167846108
- https://dash.harvard.edu/server/api/core/bitstreams/7312037d-85e6-6bd4-e053-0100007fdf3b/content
- https://neuroscience.jhu.edu/files2/publications_Rothstein_J_nihms-136480.pdf
- https://search.library.ucsf.edu/discovery/fulldisplay?docid=cdi_proquest_miscellaneous_72684329&context=PC&vid=01UCS_SAF:UCSF&lang=en&search_scope=DN_and_CI&adaptor=Primo%20Central&query=sub%2Cexact%2C%20Adenosine%20Kinase%20%2CAND&facet=citing%2Cexact%2Ccdi_FETCH-LOGICAL-c676t-b081bb8fb388dcd1305c78419b50af1b1be5ea91331d1cee6b2f9a6165f4c1e73&offset=0
- https://biochem218.stanford.edu/Projects%202007/Shelef.pdfhttp://repository.cshl.edu/id/eprint/25538/1/Methylation%20detection%20oligonucleotide%20microarray%20analysis.pdf
- https://www.bcm.edu/sites/default/files/2015/e4/bisulfite-sequencing-2012.pdf
- https://search.lib.utexas.edu/view/action/uresolver.do?operation=resolveService&package_service_id=21480684680006011&institutionId=6011&customerId=6010&VE=true
- https://med.und.edu/research/epigenetics/related-links.html
- Here are more (total 830 results) if you search 'methprimer' on academic sites only using the term "methprimer site:edu" (w/o the quotation): https://www.google.com.hk/search?q=methprimer+site:edu
- Global user base: The MethPrimer web server is accessed by thousands of researchers globally on a daily basis, making it a vital tool for the epigenetics and genomics community.
External links
[edit]