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

An efficient method for matching nucleic acid sequences.

J Felsenstein, S Sawyer, R Kochin

    Nucleic Acids Research
    |January 11, 1982
    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

    Tuberculosis among children, adolescents and young adults in the Philippines: a surveillance report.

    Western Pacific surveillance and response journal : WPSAR·2019
    Same author

    Coalescents, Phylogenies, and Likelihoods.

    The Biological bulletin·2017
    Same author

    Archaeology. The makers of the Protoaurignacian and implications for Neandertal extinction.

    Science (New York, N.Y.)·2015
    Same author

    Preoperative diagnosis of Lynch syndrome with DNA mismatch repair immunohistochemistry on a diagnostic biopsy.

    Diseases of the colon and rectum·2011
    Same author

    Evolutionary origins of the estrogen signaling system: insights from amphioxus.

    The Journal of steroid biochemistry and molecular biology·2011
    Same author

    Sequence analysis and classification of apparent recombinant begomoviruses infecting tomato in the nile and mediterranean basins.

    Phytopathology·2008
    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

    This study introduces a Fast Fourier Transform (FFT) method for calculating nucleic acid sequence matches across all alignments. The FFT algorithm offers an efficient n log n solution for long sequences, improving upon existing methods for insertions and deletions.

    Area of Science:

    • Bioinformatics
    • Computational Biology
    • Genomics

    Background:

    • Accurate comparison of nucleic acid sequences is fundamental to understanding genetic function and evolution.
    • Existing algorithms for sequence alignment, especially those allowing insertions and deletions, can be computationally intensive for long sequences.

    Purpose of the Study:

    • To develop a novel, computationally efficient method for determining the fraction of matches between two nucleic acid sequences at all possible alignments.
    • To leverage the Fast Fourier Transform (FFT) for enhanced performance in sequence matching tasks.

    Main Methods:

    • The study employs the Fast Fourier Transform (FFT) algorithm to compute sequence match fractions.
    • The computational complexity is analyzed, demonstrating a performance proportional to n ln n, where n is the length of the longer sequence.

    Related Experiment Videos

    Main Results:

    • The FFT-based method achieves a computational efficiency of O(n ln n) for comparing two nucleic acid sequences.
    • This approach is significantly faster than existing algorithms for sequence matching with insertions and deletions.
    • The method demonstrates potential for economies in matching multiple sequences, assessing complementarity, and analyzing sequences in forward and reversed orientations.

    Conclusions:

    • The FFT-based method provides a computationally efficient solution for calculating the fraction of matches between nucleic acid sequences across all alignments.
    • This technique complements existing algorithms for identifying longest matching subsequences and offers speed advantages for handling insertions and deletions.
    • The FFT approach presents versatile applications in bioinformatics, including large-scale sequence analysis and comparative genomics.