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Online tools for methylation study - (Dec/15/2004 )

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Here are some online resources for methylation study

CpG island prediction:

CpG Island Searcher

CpG Plot


CpGProD (CpG Island Promoter Detection) new
CpGProD is a mammalian-specific software which proposes to identify the promoter regions associated with CpG islands (CGIs). CpGProD uses the structural characteristics of the CGIs associated with promoters (start CGIs). In a first step, CpGProD searches for all the CGIs located over the sequences and, in a second step, CpGProD identifies start CGIs and orientation of the potential promoters.

CpG island Explorer for local installation

Promoter prediction

FirstEF: first-exon and promoter prediction program for human DNA

Promoter 2.0 Prediction Server
Promoter2.0 predicts transcription start sites of vertebrate PolII promoters in DNA sequences.

WWW Promoter Scan
Predicts Promoter regions based on scoring homologies with putative eukaryotic Pol II promoter sequences.

McPromoter MM:II -- The Markov Chain Promoter Prediction Server
McPromoter is a program aiming at the exact localization of eukaryotic RNA polymerase II transcription start sites.

Bisulfite PCR Primer Design Tools:

CpG island prediction, MSP, BSP primer design.

BSP and MSP primer design

PerlPrimer: PerlPrimer is a free, open-source GUI application written in Perl that designs primers for standard PCR, bisulphite PCR, real-time PCR (QPCR) and sequencing. It aims to automate and simplify the process of primer design. (Local installation only)

MethBlast is a similarity search program designed to explore in silico bisulfite modified DNA (either or not methylated at its CpG dinucleotides). The tool is mainly developed to find primer binding sites and hence addresses specificity for PCR based assays that use bisulfite converted DNA as input material, including bisulfite sequencing, methylation-specific PCR (MSP), combined bisulfite restriction analysis (COBRA), bisulfite-PCR-SCCP (BiPS), methylation-sensitive single-nucleotide primer extension (Ms-SNuPE), and PCR melting curve analysis. For a review of these methods, see Liu and Maekawa, Analytical Biochemistry, 2003, 317:259-265

snake-sharmer - Restriction enzyme digest of bisulfite treated DNA (COBRA): differences between methylated/unmethylated sequences


Methylation related protocols

DNA Methylation Database

DNA Methylation analysis PCR Primer Database

EPD - The Eukaryotic Promoter Database

MethTools - a collection of software tools for the analysis of bisulfite treated DNA. The software does the comparison between unconverted mother sequences and deaminated sequences, generates graphical outputs of methylation patterns and methylation density, estimates the systematic error of the experiment and searches for conserved methylated nucleotide-patterns.

List of Promoter CpG Island Hypermethylation in Cancer

You are welcome to add your own.


thanks for your informations..regarding methylation studies.
these are very useful.


New tool available: visualization and quality control of DNA methylation data from bisulphite sequencing

BiQ Analyzer a software tool for easy visualization and quality control of DNA methylation data from bisulphite sequencing.


  • End-to-end support of the analysis process: from raw sequence files to a comprehensive documentation and visualization
  • Automatically generate publication-quality lollipop diagrams
  • Integrated 1-click multiple sequence alignment
  • Automated CpG highlighting - never spend your time highlighting CpGs by hand anymore
  • Generate MethDB-compatible DNA methylation files for database submission
  • Factor 5 speedup of sequence analysis while at the same time achieving better data quality
Intended Users:
  • Anyone how works with DNA methylation data from bisulphite sequencing
  • Occasional users as well as experts (the former will benefit from the help that the program gives in order to achieve a good quality management whereas the latter will save hours and days of tedious work)
Visit our website and download the software:


Thank you for your information!
I am a new one in this field, I think those things will be helpful to me.

-Little Fox-

i am new to this field, and now i am trying to use "bisearch" to design primers for MSP, at the same time, i hope to check whether my primers also bind to other locations in genome. The results often make me confused.
Who know how to use this sofeware, and whether there are other softwares can do these jobs better than bisearch?

-jin ma-

QUOTE (jin ma @ Feb 2 2006, 07:45 AM)
whether there are other softwares can do these jobs better than bisearch?

Alternatively, you can use the original target sequence (before modification) to query genomic database such as using the NCBI blast tool and UCSC blat tool.


Warning regarding Methprimer Software

I havent started my BSP experiment yet. Still designing primers. However, when I was using Methprimer I noticed the GC% numbers were totally wrong. I think they were calculated using nucleotides before the bisulfite reaction (basically, numbers are elevated probably d/t using cytosines that should be counted as thymines). Therefore, I can't trust the calculated annealing temperatures either. I was hoping if anyone else on this board might have noticed this discrepancy. And could perhaps confirm my suspicions. The last thing I want to do is put out any misinformation.

Aargh, now I must return to eye balling my genome for primers. Take care all.


Methylprimer Express!!!!!

Hi fellow forumers, ABI have just released MethylPrimer Express for free that designs MSP and BSP primer sets, it would be interesting to see how it works.

Having trouble downloading it at the moment as I am on a Mac but will post comments about it soon!



QUOTE (pcrman @ Dec 15 2004, 11:55 PM)
Here are some online resources for methylation study

snake-sharmer - Restriction enzyme digest of bisulfite treated DNA (COBRA): differences between methylated/unmethylated sequences

It's actually Snake-charmer


Hi Jin ma
METHPRIMER...BESTEST EVER program to design met primers (free !!!)
good luck , ahh, and keep an eye on the amount of C (non CpG), in your primers.


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