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

High-performance exact algorithms for motif search.

Sanguthevar Rajasekaran1, Sudha Balla, Chun-Hsi Huang

  • 1Department of CSE, University of Connecticut, Storrs, CT 06269, USA. rajasek@engr.uconn.edu

Journal of Clinical Monitoring and Computing
|December 6, 2005
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

Associations between controlling nutritional status and mortality in osteoporosis: evidence from NHANES, 2005-2018.

Calcified tissue international·2026
Same author

Femoral Osteochondritis Dissecans and Tibial Osteochondral Defect in an Adult Revealed by Bone SPECT/CT.

Diagnostics (Basel, Switzerland)·2026
Same author

<i>Special Issue:</i> 13th International Conference on Computational Advances in Bio and Medical Sciences.

Journal of computational biology : a journal of computational molecular cell biology·2026
Same author

Fast Algorithms for Computing Jaro Similarity.

Journal of computational biology : a journal of computational molecular cell biology·2026
Same author

Cell Culture Substrate Variation Alters Extracellular Vesicle Biogenesis Without Affecting Non-Coding Repeat RNA Profile.

Small (Weinheim an der Bergstrasse, Germany)·2026
Same author

Interstellar ices as carriers of supernova material to the early solar system.

Nature communications·2025
Same journal

Not all anesthetic techniques fit the questions: editorial fit reflects scientific fit.

Journal of clinical monitoring and computing·2026
Same journal

Correction: Clinical validation of an adapted Eleveld Model for high‑dose propofol treatments for depression.

Journal of clinical monitoring and computing·2026
Same journal

Safety and efficacy of distal versus conventional radial artery cannulation for invasive blood pressure monitoring: a systematic review and meta-analysis.

Journal of clinical monitoring and computing·2026
Same journal

Data availability and usability of a remote device for vital sign monitoring on general wards and home: a single-center prospective, observational study.

Journal of clinical monitoring and computing·2026
Same journal

Nociception-guided opioid administration within multimodal analgesia for laparoscopic endometriosis surgery: a randomized controlled trial.

Journal of clinical monitoring and computing·2026
Same journal

Effect of preoperative β-blocker use on Analgesia-Nociception Index during laparoscopic cholecystectomy.

Journal of clinical monitoring and computing·2026
See all related articles

This study presents exact algorithms for the motif search problem in biological data. The novel algorithms, including SMS, DMS, and a Monte Carlo approach, offer improvements for identifying repeated patterns in large datasets.

Area of Science:

  • Bioinformatics
  • Computational Biology
  • Genomics

Background:

  • The Human Genome Project has generated vast biological data, necessitating advanced computational methods.
  • Identifying recurring patterns, or motifs, within this data is crucial for biological insight.
  • The general motif search problem is computationally challenging (NP-hard).

Purpose of the Study:

  • To address the motif search problem by developing exact algorithms.
  • To present efficient computational techniques for extracting meaningful patterns from biological sequences.
  • To focus on two specific, challenging versions of the motif search problem.

Main Methods:

  • Concentration on exact algorithmic approaches rather than heuristics.
  • Development of a sorting-based algorithm (SMS) for Problem 1.

Related Experiment Videos

  • Introduction of a deterministic (DMS) and a randomized (Monte Carlo) algorithm for Problem 2.
  • Exploration of parallelization strategies for the proposed algorithms.

    • Main Results:

    • Presentation of elegant algorithms utilizing simple data structures like arrays.
    • Successful implementation and experimental validation of the SMS algorithm.
    • Development of both deterministic and randomized exact algorithms for a more complex motif search problem.
    • Demonstration of the potential for parallelizing these motif search algorithms.

    Conclusions:

    • The proposed algorithms represent an advancement over existing methods for specific motif search problems.
    • These novel algorithms demonstrate practical applicability and potential for high performance in analyzing biological sequence data.