Download
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
Project Samples
Follow MethyMer
Other Useful Business Software
MongoDB Atlas runs apps anywhere
MongoDB Atlas gives you the freedom to build and run modern applications anywhere—across AWS, Azure, and Google Cloud. With global availability in over 115 regions, Atlas lets you deploy close to your users, meet compliance needs, and scale with confidence across any geography.
Rate This Project
Login To Rate This Project
User Reviews
Be the first to post a review of MethyMer!
