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Related Concept Videos

Genome Annotation and Assembly03:36

Genome Annotation and Assembly

The genome refers to all of the genetic material in an organism. It can range from a few million base pairs in microbial cells to several billion base pairs in many eukaryotic organisms. Genome assembly refers to the process of taking the DNA sequencing data and putting it all back together in a correct order to create a close representation of the original genome. This is followed by the identification of functional elements on the newly assembled genome, a process called genome annotation.
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...
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 18, 2026

Mapping Genome-wide Accessible Chromatin in Primary Human T Lymphocytes by ATAC-Seq
09:08

Mapping Genome-wide Accessible Chromatin in Primary Human T Lymphocytes by ATAC-Seq

Published on: November 13, 2017

BFAST: an alignment tool for large scale genome resequencing.

Nils Homer1, Barry Merriman, Stanley F Nelson

  • 1Department of Computer Science, University of California Los Angeles, Los Angeles, CA, USA.

Plos One
|November 13, 2009
PubMed
Summary
This summary is machine-generated.

A new algorithm, BFAST, rapidly and accurately aligns billions of short DNA sequences for whole human genome resequencing. It offers customizable speed and accuracy, handling errors and variations effectively.

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Last Updated: Jun 18, 2026

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Introductory Analysis and Validation of CUT&RUN Sequencing Data
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Introductory Analysis and Validation of CUT&RUN Sequencing Data

Published on: December 13, 2024

Area of Science:

  • Genomics
  • Bioinformatics
  • Computational Biology

Background:

  • Massively parallel DNA sequencing generates billions of short reads requiring efficient alignment.
  • Whole human genome resequencing necessitates rapid and accurate mapping of these reads to a reference genome.
  • Alignment accuracy is critical, especially for short reads (25-100 bp) with errors and biological variations.

Purpose of the Study:

  • Introduce BFAST, a novel algorithm and implementation for DNA sequence alignment.
  • Optimize alignment for speed and accuracy in the context of large-scale sequencing data.
  • Provide a tool that handles errors, variations, and supports parallel computation.

Main Methods:

  • Developed a new algorithm utilizing flexible, efficient whole genome indexes for rapid read mapping.
  • Implemented multiple independent indexes to enhance robustness against read errors and sequence variants.
  • Employed Smith-Waterman algorithm with gap support for local alignment and indel detection.

Main Results:

  • BFAST demonstrates superior sensitivity in alignment compared to BLAT, MAQ, SHRiMP, and SOAP, particularly for insertions and deletions.
  • The algorithm minimizes false mappings while maintaining competitive speed.
  • BFAST successfully aligned one billion reads for whole human genome resequencing in under 24 hours on a modest cluster.

Conclusions:

  • BFAST offers a significant advancement in aligning short DNA sequence reads for large-scale genomics projects.
  • The tool provides high sensitivity and accuracy, crucial for resequencing applications.
  • BFAST is freely available and efficient for processing massive sequencing datasets.