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NGSmethDB 2017: enhanced methylomes and differential methylation.

Ricardo Lebrón1,2, Cristina Gómez-Martín1,2, Pedro Carpena3

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The updated NGSmethDB database now offers whole genome methylomes from whole genome bisulfite sequencing (WGBS) data. It includes new data types for discovering epigenetic biomarkers and improved access methods for comparative analyses.

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Area of Science:

  • Genomics
  • Epigenetics
  • Bioinformatics

Background:

  • NGSmethDB is a database storing whole genome methylomes from bisulfite sequencing data.
  • Previous versions required updates to accommodate new data and analysis methods.

Purpose of the Study:

  • To present the 2017 update of the NGSmethDB database.
  • To enhance the database with new data types and improved accessibility for epigenetic biomarker discovery.

Main Methods:

  • Whole genome methylomes were generated using bisulfite sequencing (WGBS) technology.
  • Stringent quality controls and a two-step mapping process were implemented.
  • The database backend was updated to MongoDB, and track hubs and a RESTful API were introduced.

Main Results:

  • The database now stores a significantly increased number of samples.
  • Two new data types were added: differentially methylated single-cytosines and methylation segments.
  • Improved database access, visualization, and comparative analysis capabilities were achieved.

Conclusions:

  • The updated NGSmethDB provides a valuable resource for epigenetic research and biomarker discovery.
  • Enhanced accessibility and new data types facilitate comparative analyses of methylation data.