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

Using suffix tree to discover complex repetitive patterns in DNA sequences.

Dan He1

  • 1Dept. of Comput. Sci., Vermont Univ., Burlington, VT 05405, USA. hedanxkhc@hotmail.com

Conference Proceedings : ... Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Annual Conference
|October 20, 2007
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

Multicomponent Analysis of Liuwei Dihuang Pills by a Single Marker Quantification Method and Chemometric Discrimination of Fingerprints.

Journal of analytical methods in chemistry·2023
Same author

Biomarker Testing, Treatment, and Outcomes in Patients With Advanced/Metastatic Non-Small Cell Lung Cancer Using a Real-World Database.

Journal of the National Comprehensive Cancer Network : JNCCN·2023
Same author

Circadian gene ARNTL initiates circGUCY1A2 transcription to suppress non-small cell lung cancer progression via miR-200c-3p/PTEN signaling.

Journal of experimental & clinical cancer research : CR·2023
Same author

Src tyrosine kinase promotes cardiac remodeling induced by chronic sympathetic activation.

Bioscience reports·2023
Same author

Identifying prognostic markers in spatially heterogeneous breast cancer microenvironment.

Journal of translational medicine·2023
Same author

Water consumption of electric power system in China: from electricity generation to consumption.

Environmental science and pollution research international·2023
Same journal

Highly Articulated Robotic Probe for Minimally Invasive Surgery.

Conference proceedings : ... Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Annual Conference·2010
Same journal

Combined peripheral and cortical neural stimulation in motor neurorehabilitation.

Conference proceedings : ... Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Annual Conference·2008
Same journal

Embedded assessment algorithms within home-based cognitive computer game exercises for elders.

Conference proceedings : ... Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Annual Conference·2008
Same journal

Digital signal processing of the wideband external pulse recorded during cuff deflation: a new way to measure blood pressure.

Conference proceedings : ... Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Annual Conference·2008
Same journal

Immune cells detection of the in vivo rejecting heart in USPIO-enhanced magnetic resonance imaging.

Conference proceedings : ... Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Annual Conference·2008
Same journal

wHospital: a web-based application with digital signature for drugs dispensing management.

Conference proceedings : ... Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Annual Conference·2007
See all related articles

This study introduces a novel suffix tree algorithm for discovering complex repetitive patterns in DNA sequences. The new method accurately defines repeats by considering length and frequency, improving upon existing bioinformatics approaches.

Area of Science:

  • Bioinformatics
  • Computational Biology
  • Genomics

Background:

  • Discovering repetitive patterns is crucial in bioinformatics.
  • Existing methods struggle to define repeats considering both length and frequency.
  • Previous algorithms for complex repeats have limitations in scope and efficiency.

Purpose of the Study:

  • To develop a novel algorithm for revealing complex repetitive patterns in DNA sequences.
  • To address the limitations of existing methods in defining and discovering repeats.
  • To improve the time complexity for analyzing long DNA sequences.

Main Methods:

  • Utilized a suffix tree-based approach for pattern discovery.
  • Developed a new algorithm to incorporate both length and frequency factors in repeat definition.

Related Experiment Videos

  • Analyzed the time complexity of the proposed algorithm.

    • Main Results:

    • The proposed algorithm effectively reveals the complex structure of repetitive patterns.
    • Achieved a time complexity of O(n²/f²), an improvement over existing methods.
    • Successfully addressed the limitations of prior algorithms in defining and finding repeats.

    Conclusions:

    • The novel suffix tree algorithm offers a more accurate and efficient method for repetitive pattern discovery in bioinformatics.
    • This approach enhances the understanding of complex repeat structures in DNA sequences.
    • The improved time complexity makes it suitable for analyzing large-scale genomic data.