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MethyMer

Free download MethyMer Linux app to run online in Ubuntu online, Fedora online or Debian online

This is the Linux app named MethyMer whose latest release can be downloaded as MethyMer.plus.DB.v.1.1.tar.gz. It can be run online in the free hosting provider OnWorks for workstations.

Download and run online this app named MethyMer with OnWorks for free.

Follow these instructions in order to run this app:

- 1. Downloaded this application in your PC.

- 2. Enter in our file manager https://www.onworks.net/myfiles.php?username=XXXXX with the username that you want.

- 3. Upload this application in such filemanager.

- 4. Start the OnWorks Linux online or Windows online emulator or MACOS online emulator from this website.

- 5. From the OnWorks Linux OS you have just started, goto our file manager https://www.onworks.net/myfiles.php?username=XXXXX with the username that you want.

- 6. Download the application, install it and run it.

SCREENSHOTS

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MethyMer


DESCRIPTION

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


Categories

Molecular Science, Bio-Informatics

This is an application that can also be fetched from https://sourceforge.net/projects/methymer/. It has been hosted in OnWorks in order to be run online in an easiest way from one of our free Operative Systems.


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