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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.
Multi-species Conserved Sequences02:51

Multi-species Conserved Sequences

Next-generation sequencing technologies have created large genomic databases of a variety of animals and plants. Ever since the human genome project was completed, scientists studied the genome of primates, mammals, and other phylogenetically distant living beings. Such large-scale  studies have provided new insights into the evolutionary relationship between organisms.
Although the genome of each species varies greatly from each other, a few sequences are highly conserved. Such conserved DNA...
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...

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Related Experiment Video

Updated: Jun 2, 2026

Introductory Analysis and Validation of CUT&#38;RUN Sequencing Data
04:58

Introductory Analysis and Validation of CUT&RUN Sequencing Data

Published on: December 13, 2024

Sim4db and Leaff: utilities for fast batch spliced alignment and sequence indexing.

Brian Walenz1, Liliana Florea

  • 1The J. Craig Venter Institute, Rockville, MD 20850, USA.

Bioinformatics (Oxford, England)
|May 10, 2011
PubMed
Summary
This summary is machine-generated.

New software, sim4db and leaff, accelerates the gene annotation process for large-scale genome sequencing projects. These tools enable faster, more efficient batch alignments of cDNA and genomic sequences, improving gene identification accuracy.

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Area of Science:

  • Genomics
  • Bioinformatics

Background:

  • Genome sequencing projects are generating vast amounts of data requiring efficient annotation.
  • Aligning gene sequences from related species is a cost-effective method for gene identification.
  • Existing tools for sequence alignment lack the necessary sensitivity and speed for genome-wide analysis.

Purpose of the Study:

  • To present an optimized tool for batch alignment of cDNA and genomic sequences.
  • To improve the speed and efficiency of gene identification in large-scale genome annotation.

Main Methods:

  • Optimization of the sim4cc program into sim4db and leaff packages.
  • Implementation in C, C++, and Perl for Linux and Unix platforms.
  • Development of batch alignment capabilities for multiple sequence comparisons.

Main Results:

  • The new tool, sim4db and leaff, performs batch alignments significantly faster than its predecessor.
  • Achieved high accuracy in aligning cDNA and genomic sequences.
  • Demonstrated suitability for genome-wide analyses.

Conclusions:

  • Sim4db and leaff offer a highly accurate and efficient solution for genome-wide gene annotation.
  • The optimized tool addresses the limitations of previous methods in terms of speed and sensitivity.
  • Facilitates more economical and reliable gene identification in the era of large-scale sequencing.