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Related Concept Videos

Gene Evolution - Fast or Slow?02:05

Gene Evolution - Fast or Slow?

The genomes of eukaryotes are punctuated by long stretches of sequence which do not code for proteins or RNAs. Although some of these regions do contain crucial regulatory sequences, the vast majority of this DNA serves no known function. Typically, these regions of the genome are the ones in which the fastest change, in evolutionary terms, is observed, because there is typically little to no selection pressure acting on these regions to preserve their sequences.
In contrast, regions which code...
Gene Evolution - Fast or Slow?02:05

Gene Evolution - Fast or Slow?

The genomes of eukaryotes are punctuated by long stretches of sequence which do not code for proteins or RNAs. Although some of these regions do contain crucial regulatory sequences, the vast majority of this DNA serves no known function. Typically, these regions of the genome are the ones in which the fastest change, in evolutionary terms, is observed, because there is typically little to no selection pressure acting on these regions to preserve their sequences.
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Genome comparison is one of the excellent ways to interpret the evolutionary relationships between organisms. The basic principle of genome comparison is that if two species share a common feature, it is likely encoded by the DNA sequence conserved between both species. The advent of genome sequencing technologies in the late 20th century enabled scientists to understand the concept of conservation of domains between species and helped them to deduce evolutionary relationships across diverse...
Sanger Sequencing01:57

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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...
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...
RACE - Rapid Amplification of cDNA Ends02:35

RACE - Rapid Amplification of cDNA Ends

Rapid Amplification of cDNA Ends, or RACE, is one of the most effective methods to obtain a full-length cDNA from an mRNA sequence between a known internal region to the unknown sequence at the 5’ or 3’ end. The unknown region is cloned in the cDNA by a gene-specific primer that binds the known end, and a hybrid primer that attaches a predefined anchor sequence to the unknown end of the cDNA. The sequence in between is amplified by PCR with an anchor primer and a gene-specific primer.
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Related Experiment Video

Updated: Jun 13, 2026

An Integrated Approach for Microprotein Identification and Sequence Analysis
09:37

An Integrated Approach for Microprotein Identification and Sequence Analysis

Published on: July 12, 2022

Cgaln: fast and space-efficient whole-genome alignment.

Ryuichiro Nakato1, Osamu Gotoh

  • 1Department of Intelligence Science and Technology, Graduate School of Informatics, Kyoto University, Yoshida-Honmachi, Sakyo-ku, Kyoto-shi, Kyoto 606-8501, Japan.

BMC Bioinformatics
|May 4, 2010
PubMed
Summary
This summary is machine-generated.

The Cgaln program efficiently aligns large whole genomes, including mammalian genomes, on standard computers. It is faster, more memory-efficient, and comparable in accuracy to existing tools for genomic analysis.

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Area of Science:

  • Genomics
  • Bioinformatics
  • Computational Biology

Background:

  • Whole-genome sequence alignment is crucial for understanding genome function, evolution, and characteristics.
  • Rapid accumulation of genomic data necessitates efficient alignment tools for large sequences.
  • Current tools struggle with aligning large genomes like mammalian ones on conventional hardware.

Purpose of the Study:

  • To present an updated algorithm and open-source program, Cgaln, for whole-genome alignment.
  • To evaluate Cgaln's performance against existing whole-genome alignment tools.
  • To demonstrate Cgaln's capability in handling large-scale genomic comparisons.

Main Methods:

  • The study utilizes the Coarse-Grained Alignment (CGAT) algorithm, a two-step process involving block-level and nucleotide-level alignment.
  • The updated algorithm is implemented in the open-source Cgaln program.
  • Performance comparison involved whole genomic sequences of bacteria and mammalian chromosome pairs.

Main Results:

  • Cgaln demonstrates superior speed and memory efficiency compared to existing alignment programs.
  • The program achieves comparable sensitivity and accuracy to state-of-the-art tools.
  • Cgaln can align human and mouse whole genomes in under 13 hours on a standard desktop computer.

Conclusions:

  • Cgaln is a fast, memory-efficient, and effective tool for comparing large genomes, including intact chromosomal sequences.
  • The program adeptly handles genomic rearrangements.
  • Cgaln offers a novel approach to reduce computational complexity in genome science.