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Related Experiment Video

Updated: May 3, 2026

Using SCOPE to Identify Potential Regulatory Motifs in Coregulated Genes
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Efficient sequential and parallel algorithms for planted motif search.

Marius Nicolae1, Sanguthevar Rajasekaran

  • 1Department of Computer Science and Engineering, University of Connecticut, Storrs, CT, USA. marius.nicolae@engr.uconn.edu.

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|February 1, 2014
PubMed
Summary
This summary is machine-generated.

A new algorithm, PMS8, efficiently solves the challenging Planted Motif Search (PMS) problem, finding DNA or protein sequences with mismatches. This exact parallel algorithm advances motif discovery by solving previously unsolvable instances.

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Area of Science:

  • Bioinformatics
  • Computational Biology
  • Genomics

Background:

  • Motif searching is crucial for detecting rare events in DNA/protein sequences.
  • Planted Motif Search (PMS) identifies sequences of length l with at most d mismatches across n sequences.
  • The PMS problem is NP-complete, with existing algorithms facing performance gaps on challenging instances.

Purpose of the Study:

  • To present a fast, exact, and parallel algorithm for the Planted Motif Search (PMS) problem.
  • To address the performance limitations of current state-of-the-art PMS algorithms.
  • To introduce novel methods for generating common neighborhoods in motif discovery.

Main Methods:

  • Development of PMS8, a novel exact parallel algorithm for PMS.
  • Implementation of PMS8 to solve challenging (l,d) instances.
  • Comparative analysis of PMS8 against existing state-of-the-art algorithms.

Main Results:

  • PMS8 successfully solves challenging PMS instances, including (25,10) and (26,11), which were previously unsolvable.
  • The algorithm demonstrates efficiency on larger instances, such as (50,21).
  • Identified necessary and sufficient conditions for 3 l-mers to share a common d-neighbor.

Conclusions:

  • PMS8 is an efficient and exact algorithm for Planted Motif Search.
  • The algorithm's parallel implementation enhances its capabilities.
  • PMS8 significantly advances the field by solving previously intractable PMS instances.