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Updated: May 27, 2026

Using SCOPE to Identify Potential Regulatory Motifs in Coregulated Genes
07:55

Using SCOPE to Identify Potential Regulatory Motifs in Coregulated Genes

Published on: May 31, 2011

A cost-aggregating integer linear program for motif finding.

Carl Kingsford1, Elena Zaslavsky, Mona Singh

  • 1Center for Bioinformatics & Computational Biology and Department of Computer Science, University of Maryland, College Park, MD.

Journal of Discrete Algorithms (Amsterdam, Netherlands)
|November 15, 2011
PubMed
Summary
This summary is machine-generated.

This study introduces a new integer linear program to efficiently find DNA motifs, which are crucial for understanding gene regulation. The method optimizes substring similarity, aiding in the discovery of important biological sequences like transcription factor binding sites.

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Last Updated: May 27, 2026

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Peptide-based Identification of Functional Motifs and their Binding Partners
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Peptide-based Identification of Functional Motifs and their Binding Partners

Published on: June 30, 2013

Area of Science:

  • Bioinformatics
  • Computational Biology
  • Genomics

Background:

  • The motif finding problem seeks similar substrings in biological sequences, often representing regulatory elements.
  • Identifying these motifs is crucial for understanding DNA function and gene regulation.

Purpose of the Study:

  • To develop a novel computational approach for the motif finding problem.
  • To optimize the search for substrings with minimal pairwise distances within biological sequences.

Main Methods:

  • Formulated a new integer linear program (ILP) for the motif finding problem.
  • Utilized aggregate consideration of sequence position pairs based on limited distance possibilities.
  • Tightened the ILP relaxation by adding an exponential set of constraints.
  • Developed an efficient separation algorithm to solve the tightened ILP in polynomial time.

Main Results:

  • The proposed ILP effectively addresses the motif finding problem.
  • The method demonstrates practical effectiveness in identifying known transcription factor binding sites.
  • The approach allows for finding optimal solutions to the motif finding problem.

Conclusions:

  • The novel ILP framework provides an efficient and effective method for motif discovery.
  • This approach enhances the ability to uncover regulatory elements in DNA sequences.
  • The computational strategy is valuable for genomic research and understanding gene regulation.