ampliMethProfiler: a pipeline for the analysis of CpG methylation profiles of targeted deep bisulfite sequenced amplicons

BMC Bioinformatics
Giovanni ScalaSergio Cocozza

Abstract

CpG sites in an individual molecule may exist in a binary state (methylated or unmethylated) and each individual DNA molecule, containing a certain number of CpGs, is a combination of these states defining an epihaplotype. Classic quantification based approaches to study DNA methylation are intrinsically unable to fully represent the complexity of the underlying methylation substrate. Epihaplotype based approaches, on the other hand, allow methylation profiles of cell populations to be studied at the single molecule level. For such investigations, next-generation sequencing techniques can be used, both for quantitative and for epihaplotype analysis. Currently available tools for methylation analysis lack output formats that explicitly report CpG methylation profiles at the single molecule level and that have suited statistical tools for their interpretation. Here we present ampliMethProfiler, a python-based pipeline for the extraction and statistical epihaplotype analysis of amplicons from targeted deep bisulfite sequencing of multiple DNA regions. ampliMethProfiler tool provides an easy and user friendly way to extract and analyze the epihaplotype composition of reads from targeted bisulfite sequencing experiments. ampliMethPr...Continue Reading

References

May 17, 2006·Trends in Ecology & Evolution·Susan Kalisz, Michael D Purugganan
Apr 7, 2007·Pediatric Research·Dana C DolinoyRandy L Jirtle
Dec 17, 2009·BMC Bioinformatics·Christiam CamachoThomas L Madden
Apr 13, 2010·Nature Methods·J Gregory CaporasoRob Knight
Feb 1, 2011·Bioinformatics·Robert Schmieder, Robert Edwards
Oct 22, 2013·Bioinformatics·Jiajie ZhangAlexandros Stamatakis
May 20, 2015·Bioinformatics and Biology Insights·Anastasis OulasIoannis Iliopoulos

Related Concepts

H2S(D2S)
Metazoa
DNA, Double-Stranded
Computer Programs and Programming
Sulfites
Sequence Determinations, DNA
CpG Clusters
DNA Methylation
Gastrointestinal Tract Structure
D-Aspartate oxidase

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