对基因甲基化分析感兴趣的请进！
丁香园论坛
2306
大伙好，我购买Chemicon公司的CpGenome DNA Modificatio Kit 打算五月开始做，希望以后一起交流一下甲基化分析的实验技术。
QQ：395848659
Here are some online resources for methylation study
CpG island prediction:
CpG Island Searcher
CpG Plot
MethPrimer
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 http://bioinfo.hku.hk/cpgieintro.html
Promoter prediction
FirstEF: first-exon and promoter prediction program for human DNA
http://rulai.cshl.org/tools/FirstEF/
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:
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/cgrunau/methods/snake_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/
EPD - The Eukaryotic Promoter Database
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.edu/~hypermet/list_of_promoters.htm
You are welcome to add your own.
QQ：395848659
Here are some online resources for methylation study
CpG island prediction:
CpG Island Searcher
CpG Plot
MethPrimer
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 http://bioinfo.hku.hk/cpgieintro.html
Promoter prediction
FirstEF: first-exon and promoter prediction program for human DNA
http://rulai.cshl.org/tools/FirstEF/
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:
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/cgrunau/methods/snake_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/
EPD - The Eukaryotic Promoter Database
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.edu/~hypermet/list_of_promoters.htm
You are welcome to add your own.
