PacBio Whole Genome Methylation Analysis

PacBio Whole Genome Methylation Analysis

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As a bioinformatics data analysis provider, CD Genomics offers comprehensive whole genome methylation analysis services to directly and easily detect whole genome methylation profiles to help you understand and leverage the epigenomics landscape. Our high-quality data analysis platform will be used to generate high-quality analysis results in a fast analysis cycle.

Introduction to Whole Genome Methylation Analysis

DNA methylation is key to the control of several biological phenomena in eukaryotes and prokaryotes, from cell differentiation to the control of gene flow, pathogenesis and virulence. Third-generation sequencing technologies (PacBio SMRT and Nanopore sequencing) allow direct identification of the most commonly methylated bases. These approaches are rapidly increasing the number of studies of whole genome DNA methylation. Analysis of whole genome DNA methylation is critical to understanding the impact of methylation in normal biology and in diseases, including cancer. whole genome analyses, such as microarray and next-generation sequencing technologies, have been used to assess most of the methylationome. Interest is growing in computational pipelines that can mine DNA methylation signatures in a whole genome manner. Recently, three software packages have been released allowing visualization of methylation profiles from SMRT or ONT sequencing data.

Fig. 1. Schematic of the procedures for whole genome DNA methylation analysis.Fig. 1. Schematic of the procedures for whole genome DNA methylation analysis. (Lee J R, et al, 2018)

Application Field

Our whole genome methylation analysis can be used for but not limited to the following research:

Epigenetics and developmental biology: our PacBio whole genome methylation bioinformatics analysis can reveal the complex epigenetic changes behind developmental processes and identify the key regulatory elements involved.

Cancer epigenetics: our PacBio whole genome methylation bioinformatics analysis provides a comprehensive view of cancer-associated methylation alterations. This information can help identify potential biomarkers, understand mechanisms of carcinogenesis, and develop targeted therapies.

Environmental epigenomics: our PacBio whole genome methylation bioinformatics analysis can help you study the impact of environmental exposures, such as pollutants or dietary factors, on DNA methylation profiles.

Agriculture and crop improvement: our PacBio whole genome methylation bioinformatics analysis can help you study DNA methylation variation associated with crop traits, stress responses, and environmental adaptations. This knowledge can be used to develop crops with higher yields, resilience, and nutritional quality.

CD Genomics Data Analysis Pipeline:

Based on PacBio SMRT sequencing platform, CD Genomics offers state-of-the-art services for whole genome methylation bioinformatics analysis to explore DNA methylation patterns and their impact on gene regulation, development, disease, and environmental interactions. Our workflow is as follows:

(1) Data processing and quality control

CD Genomics employs stringent quality control measures to ensure the reliability and accuracy of sequencing data. We perform data pre-processing, including read trimming, error correction and quality filtering to improve overall data quality and reduce sequencing artifacts.

(2) Read mapping and methylation calling

CD Genomics utilizes advanced alignment algorithms to map long sequencing reads to the reference genome. This step identifies methylated cytosine residues and their genomic location. Our skilled bioinformatics team uses sophisticated methylation identification algorithms to accurately quantify DNA methylation levels and generate base-resolution methylation profiles.

(3) Differential methylation analysis

To identify differential methylation patterns, CD Genomics performs statistical analysis of methylation data. We use  obust statistical models and hypothesis testing to identify differentially methylated regions (DMRs) between different experimental conditions or sample groups.

(4) Functional annotation and interpretation

CD Genomics provides comprehensive functional annotation and interpretation of methylation data. We combine methylation information with genomic annotations, such as gene annotations, enhancer regions and regulatory elements.

Whole Genome Methylation Analysis Content:

Detection of Different Types of Base Modification Sites State-of-the-art algorithms and software tools are used to identify and quantify base modification sites for DNA methylation throughout the genome.
Base Modification Analysis Analyze and understand the distribution and function of base modifications, such as DNA methylation and other covalent modifications, that occur on DNA and RNA molecules.
Regional Analysis of Differential Methylation We offer differential methylation analysis to identify methylation changes associated with various biological conditions or disease states.
Functional Analysis of Base-Modified Genes Integrate methylation data with other genomic information to gain a comprehensive understanding of the functional consequences of DNA methylation and its interactions with other epigenetic modifications.

How It Works

CD Genomics is a high-tech company specializing in multiomic data analysis. We provide services such as project design, data analysis, and database construction. With a focus on developing breakthrough products and services, we are a pioneer in the biotechnology industry, serving researchers and partners worldwide.

How It Works

CD Genomics provides cutting-edge services for PacBio whole genome methylation bioinformatics analysis, enabling researchers to unravel the complex world of DNA methylation. Partnering with CD Genomics deepens the understanding of DNA methylation and opens up new avenues of genomics and epigenomics research. If you are interested in our services, please contact us for more detailed information.


  1. Lee J R, Ryu D S, Park S J, et al. Successful application of human-based methyl capture sequencing for methylome analysis in non-human primate models[J]. BMC genomics, 2018, 19(1): 1-12.
* For Research Use Only. Not for use in diagnostic procedures.
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