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

Multiseed lossless filtration.

Gregory Kucherov1, Laurent Noé, Mikhail Roytberg

  • 1INRIA/LORIA, 615, rue du Jardin Botanique, B.P. 101, 54602 Villers-lès-Nancy, France. Gregory.Kucherov@loria.fr

IEEE/ACM Transactions on Computational Biology and Bioinformatics
|October 19, 2006
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

Efficient and robust search of microbial genomes via phylogenetic compression.

Nature methods·2025
Same author

Efficient and Robust Search of Microbial Genomes via Phylogenetic Compression.

bioRxiv : the preprint server for biology·2023
Same author

Porechop_ABI: discovering unknown adapters in Oxford Nanopore Technology sequencing reads for downstream trimming.

Bioinformatics advances·2023
Same author

Space-efficient representation of genomic k-mer count tables.

Algorithms for molecular biology : AMB·2022
Same author

Set-Min Sketch: A Probabilistic Map for Power-Law Distributions with Application to <i>k</i>-Mer Annotation.

Journal of computational biology : a journal of computational molecular cell biology·2022
Same author

Simplitigs as an efficient and scalable representation of de Bruijn graphs.

Genome biology·2021

This study introduces a new seed-based filtration method for approximate string matching using multiple spaced seeds. This approach enhances bioinformatics applications like oligonucleotide selection.

Area of Science:

  • Bioinformatics
  • Computational Biology
  • Algorithm Design

Background:

  • Approximate string matching is crucial for bioinformatics tasks.
  • Existing methods often rely on single spaced seeds, limiting efficiency.
  • Need for improved filtration techniques in large-scale sequence analysis.

Purpose of the Study:

  • To develop and evaluate a novel seed-based filtration method for approximate string matching.
  • To explore the use of multiple spaced seeds for enhanced performance.
  • To apply the method to practical bioinformatics problems, such as oligonucleotide selection.

Main Methods:

  • Simultaneous utilization of multiple spaced seeds for filtration.
  • Development of algorithms to compute seed family parameters.

Related Experiment Videos

  • Investigation of combinatorial properties of seed families.
  • Construction techniques for efficient seed families.

    • Main Results:

    • The proposed method demonstrates effectiveness in approximate string matching.
    • Algorithms for parameter computation and family construction are presented.
    • Successful large-scale application to oligonucleotide selection for EST databases.

    Conclusions:

    • Multiple spaced seeds offer advantages over single seeds in filtration.
    • The developed techniques provide efficient solutions for bioinformatics challenges.
    • This method has significant potential for improving sequence database analysis.