Jove
Visualize
Contact Us
JoVE
x logofacebook logolinkedin logoyoutube logo
ABOUT JoVE
OverviewLeadershipBlogJoVE Help Center
AUTHORS
Publishing ProcessEditorial BoardScope & PoliciesPeer ReviewFAQSubmit
LIBRARIANS
TestimonialsSubscriptionsAccessResourcesLibrary Advisory BoardFAQ
RESEARCH
JoVE JournalMethods CollectionsJoVE Encyclopedia of ExperimentsArchive
EDUCATION
JoVE CoreJoVE BusinessJoVE Science EducationJoVE Lab ManualFaculty Resource CenterFaculty Site
Terms & Conditions of Use
Privacy Policy
Policies

Related Experiment Videos

MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform.

Kazutaka Katoh1, Kazuharu Misawa, Kei-ichi Kuma

  • 1Department of Biophysics, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan.

Nucleic Acids Research
|July 24, 2002
PubMed
Summary
This summary is machine-generated.

Related Concept Videos

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by
Same author

Peculiar pigment pattern and population profile of a poisonous pufferfish.

PeerJ·2026
Same author

Characteristic pathological findings of achalasia behind unresectable esophageal cancer with pathological complete response after chemotherapy: a case report and literature review.

BMC gastroenterology·2026
Same author

Polymeric soft materials with molecular recognition: from static binding to dynamic functions in gels, particles, and interfaces.

Science and technology of advanced materials·2026
Same author

Machine learning-based prediction of impaired arginine vasopressin secretion during hypertonic saline test.

Endocrine journal·2026
Same author

A case of multiple type I endocrine neoplasia with gastrin-producing and glucagon-producing tumors successfully resected 18 years after insulinoma surgery.

Clinical journal of gastroenterology·2026
Same author

Recurrent hemorrhagic pancreatic pseudocyst with superior mesenteric vein thrombosis treated by pancreaticoduodenectomy and vein graft reconstruction: a case report.

International journal of surgery case reports·2026
Same journal

Correction to 'scSuperAnnotator: A platform for benchmarking comparison and visualizing automated cellular annotation methods for scRNA-seq data'.

Nucleic acids research·2026
Same journal

Correction to 'Differentiable partition function calculation for RNA'.

Nucleic acids research·2026
Same journal

Deployment of non-canonical splicing in tunicate genomes is mediated by divergent U2AF function and changing m6A modification in U1 and U6 snRNA.

Nucleic acids research·2026
Same journal

Bacillus subtilis DnaB forms multiple protein-protein interactions essential for DNA replication initiation.

Nucleic acids research·2026
Same journal

Multiple forms of protein-protein and DNA binding are exhibited by BrxC from the BREX phage restriction system.

Nucleic acids research·2026
Same journal

Biosynthesis of glycosylated 5-hydroxycytosine in the DNA of diverse viruses.

Nucleic acids research·2026
See all related articles

MAFFT is a novel multiple sequence alignment program that significantly reduces CPU time using fast Fourier transform (FFT) and a simplified scoring system. It offers accurate alignments for diverse sequences, outperforming existing methods.

Area of Science:

  • Bioinformatics
  • Computational Biology
  • Genomics

Background:

  • Multiple sequence alignment (MSA) is crucial for understanding protein and nucleic acid evolution.
  • Existing MSA methods can be computationally intensive, limiting their application to large datasets.
  • Need for faster and accurate MSA algorithms is critical in modern biological research.

Purpose of the Study:

  • To develop a novel multiple sequence alignment program, MAFFT.
  • To significantly reduce computational time (CPU time) for sequence alignment.
  • To maintain or improve alignment accuracy, especially for challenging datasets.

Main Methods:

  • Implementation of MAFFT utilizing two novel techniques.
  • Rapid identification of homologous regions using Fast Fourier Transform (FFT) on amino acid volume and polarity values.

Related Experiment Videos

  • Application of a simplified scoring system to enhance speed and accuracy.
  • Development of two heuristics: FFT-NS-2 (progressive) and FFT-NS-i (iterative refinement).

    • Main Results:

    • MAFFT demonstrates drastically reduced CPU time compared to existing methods.
    • FFT-NS-2 shows comparable accuracy to CLUSTALW with significantly reduced CPU time.
    • FFT-NS-i is over 100 times faster than T-COFFEE for datasets exceeding 60 sequences, without accuracy loss.
    • The simplified scoring system improves alignment accuracy for sequences with large insertions/extensions and distantly related sequences.

    Conclusions:

    • MAFFT provides a highly efficient and accurate solution for multiple sequence alignment.
    • The novel FFT-based approach and simplified scoring system are key to MAFFT's performance gains.
    • MAFFT is a valuable tool for large-scale genomic and proteomic analyses, accelerating biological discovery.