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Related Concept Videos

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.
Maxam-Gilbert Sequencing01:05

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.
Challenges of the Maxam-Gilbert Method
The...
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...
Ribosome Profiling02:24

Ribosome Profiling

Ribosome profiling or ribo-sequencing is a deep sequencing technique that produces a snapshot of active translation in a cell. It selectively sequences the mRNAs protected by ribosomes to get an insight into a cell’s translation landscape at any given point in time.
Applications of ribosome profiling
Ribosome profiling has many applications, including in vivo monitoring of translation inside a particular organ or tissue type and quantifying new protein synthesis levels.
The technique helps...

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Updated: May 17, 2026

Pyrosequencing: A Simple Method for Accurate Genotyping
13:06

Pyrosequencing: A Simple Method for Accurate Genotyping

Published on: January 8, 2008

BIGrat: a repeat resolver for pyrosequencing-based re-sequencing with Newbler.

Tongwu Zhang1, Yingfeng Luo, Yaping Chen

  • 1CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100029, China.

BMC Research Notes
|October 17, 2012
PubMed
Summary
This summary is machine-generated.

We developed BIGrat (Beijing Institute of Genomics Re-Assembly Tool), a new genome assembly tool for pyrosequencing data. BIGrat enhances existing pipelines, improving genome assembly accuracy for projects using Roche 454 and IonTorrent platforms.

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Area of Science:

  • Genomics
  • Bioinformatics

Background:

  • Reference genome assembly is practical for individual genomes from raw read data.
  • Current assembly tools primarily focus on de novo assembly.
  • Newbler, a commercial tool for Roche 454, struggles with genomes containing large repeat regions.

Purpose of the Study:

  • To develop a novel sequence assembly tool for pyrosequencing-based re-sequencing projects.
  • To improve upon the limitations of existing tools like Newbler, particularly in handling repetitive genomic regions.

Main Methods:

  • Development of BIGrat (Beijing Institute of Genomics Re-Assembly Tool).
  • Utilizing pyrosequencing data from platforms such as Roche 454 and IonTorrent.
  • Integration into existing Newbler pipelines for comparative analysis.

Main Results:

  • BIGrat demonstrates improved performance compared to Newbler in genome assembly.
  • Successful evaluation on diverse genome types: chloroplast, mitochondrial, bacterial, and plant nuclear genomes.
  • BIGrat effectively handles challenges posed by large repeat regions in genome assembly.

Conclusions:

  • BIGrat is a novel sequence assembly tool designed for pyrosequencing data.
  • The tool enhances re-sequencing projects and can be integrated into Newbler pipelines.
  • BIGrat offers improved genome assembly for various organisms, especially in the presence of repeat regions.