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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...
Next-generation Sequencing03:00

Next-generation Sequencing

The first human genome sequencing project cost $2.7 billion and was declared complete in 2003, after 15 years of international cooperation and collaboration between several research teams and funding agencies. Today, with the advent of next-generation sequencing technologies, the cost and time of sequencing a human genome have dropped over 100 fold.
Next-Generation Sequencing Methods
Although all next-generation methods use different technologies, they all share a set of standard features.

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Related Experiment Video

Updated: Jun 14, 2026

Pyrosequencing for Microbial Identification and Characterization
12:37

Pyrosequencing for Microbial Identification and Characterization

Published on: August 22, 2013

Identifying and removing artificial replicates from 454 pyrosequencing data.

Tracy K Teal1, Thomas M Schmidt

  • 1Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI 48824, USA. tkteal@msu.edu

Cold Spring Harbor Protocols
|April 3, 2010
PubMed
Summary
This summary is machine-generated.

454 pyrosequencing creates artificial DNA sequence duplicates, overrepresenting over 10% of templates. A new tool using cd-hit removes these artificial replicates for accurate metagenomic and transcriptomic analysis.

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Area of Science:

  • Genomics
  • Bioinformatics
  • Molecular Biology

Background:

  • 454 pyrosequencing technology can introduce artificial sequence replication.
  • This artifact leads to overrepresentation of DNA sequencing templates by over 10%.

Purpose of the Study:

  • To address the issue of artificial sequence replication in 454 pyrosequencing data.
  • To develop a method for identifying and removing these artificial replicates.

Main Methods:

  • Developed a web-based tool utilizing the cd-hit clustering algorithm.
  • The tool identifies and removes artificially replicated sequences from 454 pyrosequencing datasets.

Main Results:

  • The tool effectively identifies and removes artificial replicates.
  • This ensures accurate sequence abundance enumeration for downstream analyses.
  • The method is suitable for standard pyrosequencing data, excluding those with prior PCR amplification.

Conclusions:

  • Removing artificial replicates is crucial for accurate comparative community, transcriptional, and metagenomic analyses.
  • The developed tool provides a reliable method for data cleaning in 454 pyrosequencing.
  • This facilitates more precise biological interpretations from sequencing data.