MethTools--a Toolbox to Visualize and Analyze DNA Methylation Data

Overview

Journal Nucleic Acids Res

Publisher Oxford University Press

Specialty Biochemistry

Date 2000 Feb 10

PMID 10666443

Citations 29

Authors

C Grunau

R Schattevoy

N Mache

A Rosenthal

Affiliations

Soon will be listed here.

Abstract

The Bisulfite Genomic Sequencing technique has found wide acceptance for the generation of DNA-methylation maps with single-base resolution. The method is based on the selective deamination of cytosine to uracil (and subsequent conversion to thymine via PCR), whereas 5-methylcytosine residues remain unchanged. Methylation maps are created by the comparison of bisulfite converted sequences with the untreated genomic sequence. 'MethTools' is a collection of software tools that replaces the time-consuming manual comparison process, generates graphical outputs of methylation patterns and methyl-ation density, estimates the systematic error of the experiment and searches for conserved methylated nucleotide patterns. The programs are written in Perl 5 and C, and the source code can be downloaded. All tools run independently but the programs are interfaced. Thus, a script can perform the entire analysis procedure automatically. In addition, a web-based remote analysis service is offered. Both the source code and the remote analysis are available at http://genome.imb-jena.de/methtools/

Citing Articles

ABSP: an automated R tool to efficiently analyze region-specific CpG methylation from bisulfite sequencing PCR.

Denoulet M, Brule M, Anquez F, Vincent A, Schnipper J, Adriaenssens E Bioinformatics. 2023; 39(1).

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Novel role of UHRF1 in the epigenetic repression of the latent HIV-1.

Verdikt R, Bendoumou M, Bouchat S, Nestola L, Pasternak A, Darcis G EBioMedicine. 2022; 79:103985.

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Increased Expression of Plasma-Induced ABCC1 mRNA in Cystic Fibrosis.

Ideozu J, Zhang X, Pan A, Ashrafi Z, Woods K, Hessner M Int J Mol Sci. 2017; 18(8).

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The Biomphalaria glabrata DNA methylation machinery displays spatial tissue expression, is differentially active in distinct snail populations and is modulated by interactions with Schistosoma mansoni.

Geyer K, Niazi U, Duval D, Cosseau C, Tomlinson C, Chalmers I PLoS Negl Trop Dis. 2017; 11(5):e0005246.

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Small-Magnitude Effect Sizes in Epigenetic End Points are Important in Children's Environmental Health Studies: The Children's Environmental Health and Disease Prevention Research Center's Epigenetics Working Group.

Breton C, Marsit C, Faustman E, Nadeau K, Goodrich J, Dolinoy D Environ Health Perspect. 2017; 125(4):511-526.

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