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MethyMer is a Python-based tool aimed at selecting specific primers for amplification of complete CpG islands. These regions are difficult in terms of selection appropriate primers because of their low-complexity, polyN-, CG-richness, etc.
MethyMer have a flexible scoring system capable of selecting primers in problematic regions (e.g. SpG islands) and includes specificity test (based on bowtie alignment against bisulfite-treated genome).
It also incorporates TCGA CpG methylation (microarrays) and gene expression (RNA-Seq) data, as well as methylation-expression correlation analysis results for 20 human cancer types.
ENCODE genome regions annotation data are also integrated in MethyMer
Features
- picking combinations of primer pairs capable of amplifying complete CpG island or other target genomic regions;
- flexible and tweakable scoring system
- specificity test
- integrated CpG methylation data (Illumina Infinium Human Methylation 450K microarrays) for 20 tumor types, derived from TCGA
- integrated TCGA RNA-Seq – CpG methylation associations study data
- visualization: CG content plot, score plot, primer specificity plot, ENCODE genome annotation, TCGA data
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