3 replies to this topic

[pcrman]

Here are some online resources for methylation study

CpG island prediction:

CpG Island Searcher

CpG Plot

MethPrimer

CpG island Explorer for local installation http://bioinfo.hku.hk/cpgieintro.html

Primer Design:

MethPrimer
CpG island prediction, MSP, BSP primer design.

BiSearch
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
http://195.83.84.240...ke_sharmer.html

Protocols:

Methylation related protocols

Database
DNA Methylation Database http://www.methdb.de/

DNA Methylation analysis PCR Primer Database http://medgen.ugent.be/methprimerdb/

Others
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.
http://genome.imb-jena.de/methtools/

List of Promoter CpG Island Hypermethylation in Cancer
http://www.missouri....f_promoters.htm

You are welcome to add your own.

[methylnick]

Here is a new program available for the presentation of bisulphite sequencing data, to be published in Biotechniques soon.


Bisulphite Analysis Suite

[vmiguel]

any tool to predict sites of methylation in plants?

[Jeronimas]

Maybe this one for plants: http://www.gmi.oeaw....n/cymate-index/

vmiguel, on 09 March 2010 - 05:12 PM, said:

any tool to predict sites of methylation in plants?