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Maxam-Gilbert Sequencing

Maxam-Gilbert Sequencing

In the same year as the discovery of the Sanger sequencing method, another group of scientists, Allan Maxam and Walter Gilbert, demonstrated their chemical-cleavage method for DNA sequencing. The Maxam-Gilbert method relies on using different chemicals that can cleave the DNA sequence at specific sites, the separation of resulting DNA fragments of variable size using electrophoresis, and deciphering the DNA sequence from the resulting gel bands.
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Enhanced Reduced Representation Bisulfite Sequencing for Assessment of DNA Methylation at Base Pair Resolution

Enhanced Reduced Representation Bisulfite Sequencing for Assessment of DNA Methylation at Base Pair Resolution

Published on: February 24, 2015

MethylCoder: software pipeline for bisulfite-treated sequences.

Brent Pedersen¹, Tzung-Fu Hsieh, Christian Ibarra

¹Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA. bpederse@gmail.com

Bioinformatics (Oxford, England)

|July 5, 2011

Summary

This summary is machine-generated.

MethylCoder is a new software tool that generates per-base methylation data from bisulfite sequencing reads. It offers flexibility and efficiency for analyzing DNA methylation patterns.

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DNA Methylation: Bisulphite Modification and Analysis

DNA Methylation: Bisulphite Modification and Analysis

Published on: October 21, 2011

Area of Science:

Bioinformatics
Computational Biology
Genomics

Background:

DNA methylation analysis is crucial for understanding gene regulation and disease.
Existing software for processing bisulfite sequencing data can be limited in flexibility and compatibility.
Efficient and accurate tools are needed for generating per-base methylation data.

Purpose of the Study:

To introduce MethylCoder, a novel software program for generating per-base methylation data.
To provide a flexible and efficient alternative to existing bisulfite sequencing analysis tools.
To enable seamless integration with common high-throughput sequencing analysis pipelines.

Main Methods:

MethylCoder utilizes existing short-read aligners, supporting soft-masked alignments and paired-end reads.
The software processes bisulfite-treated sequencing reads to identify methylation status at each base.
Output is provided in multiple formats, including text, binary, and SAM, for broad usability.

Main Results:

MethylCoder demonstrates flexibility by supporting multiple aligners and output formats.
The software is competitive in terms of processing speed and memory usage.
It facilitates downstream analysis by producing compatible data formats.

Conclusions:

MethylCoder offers a flexible, efficient, and user-friendly solution for per-base DNA methylation analysis.
Its compatibility with existing tools enhances its utility in genomics research.
The software contributes to advancing the analysis of epigenomic data.