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Related Concept Videos

RNA-seq03:21

RNA-seq

RNA sequencing, or RNA-Seq, is a high-throughput sequencing technology used to study the transcriptome of a cell. Transcriptomics helps to interpret the functional elements of a genome and identify the molecular constituents of an organism. Additionally, it also helps in understanding the development of an organism and the occurrence of diseases. 
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while microarray-based...
Sanger Sequencing01:57

Sanger Sequencing

DNA sequencing is a fundamental technique that is routinely used in the biological sciences. This method can be applied to a range of questions at different scales - from the sequencing of a cloned DNA fragment or the study of a mutation in a gene up to whole-genome sequencing. However, despite the widespread use of sequencing today, it was not until 1977 that Fredrick Sanger and his collaborators developed the chain-termination method to decode DNA sequences. It relies on the separation of a...

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Related Experiment Video

Updated: Jun 12, 2026

Enhanced Reduced Representation Bisulfite Sequencing for Assessment of DNA Methylation at Base Pair Resolution
13:47

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

Published on: February 24, 2015

An alignment algorithm for bisulfite sequencing using the Applied Biosystems SOLiD System.

Brian D Ondov1, Charles Cochran, Mark Landers

  • 1National Biodefense Analysis and Countermeasures Center, 110 Thomas Johnson Drive, Frederick, MD 21702, USA.

Bioinformatics (Oxford, England)
|June 22, 2010
PubMed
Summary
This summary is machine-generated.

A new algorithm, SOCS-B, enables accurate cytosine methylation detection using the SOLiD System. This bioinformatics tool overcomes alignment challenges, improving bisulfite sequencing sensitivity.

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Related Experiment Videos

Last Updated: Jun 12, 2026

Enhanced Reduced Representation Bisulfite Sequencing for Assessment of DNA Methylation at Base Pair Resolution
13:47

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Published on: February 24, 2015

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Optimized Analysis of DNA Methylation and Gene Expression from Small, Anatomically-defined Areas of the Brain

Published on: July 12, 2012

Area of Science:

  • Epigenetics
  • Genomics
  • Bioinformatics

Background:

  • Cytosine methylation is a key epigenetic marker detected through bisulfite sequencing.
  • The Applied Biosystems SOLiD System offers unique di-base encoding for nucleotide substitution detection.
  • Existing alignment tools struggle with SOLiD's di-base encoding for bisulfite sequencing data.

Purpose of the Study:

  • To develop a novel alignment algorithm for the SOLiD System to facilitate bisulfite sequencing.
  • To address the challenge of aligning reads with high nucleotide substitutions caused by bisulfite treatment and SOLiD's encoding.

Main Methods:

  • Presentation of SOCS-B, a reference-based, un-gapped alignment algorithm.
  • The algorithm is designed to tolerate bisulfite-induced substitutions and sequencing errors.
  • Integration of SOCS-B into the existing SOCS alignment tool.

Main Results:

  • SOCS-B successfully aligns bisulfite sequencing data from Arabidopsis thaliana enriched for CpG methylation.
  • Demonstrated a 2-fold increase in sensitivity for aligning SOLiD bisulfite data compared to existing methods.
  • Facilitates the realization of the SOLiD platform's potential for bisulfite sequencing applications.

Conclusions:

  • SOCS-B enhances the utility of the SOLiD System for bisulfite sequencing.
  • The algorithm improves the sensitivity and accuracy of epigenetic marker detection.
  • This advancement supports more effective epigenetic research using SOLiD sequencing data.