methymer

We have hosted the application methymer in order to run this application in our online workstations with Wine or directly.

Quick description about methymer:

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

User interface: Console/Terminal.
Programming Language: Python.
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