ArticleNucleic acids research2012
A mostly traditional approach improves alignment of bisulfite-converted DNA.
Article in Nucleic acids research, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 30 papers.
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Who cites it
30 citing papers in PubMed.
- Probabilistic alignment leads to improved accuracy and read coverage for bisulfite sequencing data.BMC bioinformatics · 2013Trial
- HBCR_DMR: A Hybrid Method Based on Beta-Binomial Bayesian Hierarchical Model and Combination of Ranking Method to Detect Differential Methylation Regions in Bisulfite Sequencing Data.Journal of personalized medicine · 2024Article
- Efficiently quantifying DNA methylation for bulk- and single-cell bisulfite data.Bioinformatics (Oxford, England) · 2023Article
- Analysis and Performance Assessment of the Whole Genome Bisulfite Sequencing Data Workflow: Currently Available Tools and a Practical Guide to Advance DNA Methylation Studies.Small methods · 2022Review
- Low guanine content and biased nucleotide distribution in vertebrate mtDNA can cause overestimation of non-CpG methylation.NAR genomics and bioinformatics · 2022Article
- Computational challenges in detection of cancer using cell-free DNA methylation.Computational and structural biotechnology journal · 2022Review
- Analysis of Bisulfite Sequencing Data Using Bismark and DMRcaller to Identify Differentially Methylated Regions.Methods in molecular biology (Clifton, N.J.) · 2022Article
- Comprehensive benchmarking of software for mapping whole genome bisulfite data: from read alignment to DNA methylation analysis.Briefings in bioinformatics · 2021Article
- An effective method to resolve ambiguous bisulfite-treated reads.BMC bioinformatics · 2021Article
- Article
- methCancer-gen: a DNA methylome dataset generator for user-specified cancer type based on conditional variational autoencoder.BMC bioinformatics · 2020Article
- How sequence alignment scores correspond to probability models.Bioinformatics (Oxford, England) · 2020Article
- DNA methylation data by sequencing: experimental approaches and recommendations for tools and pipelines for data analysis.Clinical epigenetics · 2019Review
- Epigenetic control of gene regulation during development and disease: A view from the retina.Progress in retinal and eye research · 2018Review
- EAGLE: Explicit Alternative Genome Likelihood Evaluator.BMC medical genomics · 2018Article
- Evaluation of preprocessing, mapping and postprocessing algorithms for analyzing whole genome bisulfite sequencing data.Briefings in bioinformatics · 2016Article
- Targeted alignment and end repair elimination increase alignment and methylation measure accuracy for reduced representation bisulfite sequencing data.BMC genomics · 2016Article
- ALP & FALP: C++ libraries for pairwise local alignment E-values.Bioinformatics (Oxford, England) · 2016Article
- Integrating Epigenomics into the Understanding of Biomedical Insight.Bioinformatics and biology insights · 2016Review
- RNF: a general framework to evaluate NGS read mappers.Bioinformatics (Oxford, England) · 2016Article
Corrections and comments
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Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Cytosines in genomic DNA are sometimes methylated. This affects many biological processes and diseases. The standard way of measuring methylation is to use bisulfite, which converts unmethylated cytosines to thymines, then sequence the DNA and compare it to a reference genome sequence. We describe a method for the critical step of aligning the DNA reads to the correct genomic locations. Our method builds on classic alignment techniques, including likelihood-ratio scores and spaced seeds. In a realistic benchmark, our method has a better combination of sensitivity, specificity and speed than nine other high-throughput bisulfite aligners. This study enables more accurate and rational analysis of DNA methylation. It also illustrates how to adapt general-purpose alignment methods to a special case with distorted base patterns: this should be informative for other special cases such as ancient DNA and AT-rich genomes.
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Registered trials
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