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Related Concept Videos

Conservation of Protein Domains02:26

Conservation of Protein Domains

Protein domains are small structurally independent units that are part of a single amino acid chain.  Although these domains are often structurally independent, they may rely on synergistic effects to perform their functions as part of a larger protein. Protein domains may be conserved within the same organism, as well as across different organisms.
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Cis-regulatory sequences are short fragments of non-coding DNA that are present on the same chromosomes as the genes that they regulate. These fragments serve as binding sites for transcriptional regulators, proteins that are responsible for controlling gene transcription and differential gene expression across cell types in eukaryotes. Cis-regulatory sequences can be close to the gene of interest or thousands of bases away in the DNA sequence; however, those sequences that are further away are...
Cis-regulatory Sequences02:02

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Related Experiment Video

Updated: Jul 15, 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

SCOPE: a web server for practical de novo motif discovery.

Jonathan M Carlson1, Arijit Chakravarty, Charles E DeZiel

  • 1Department of Computer Science and Engineering, University of Washington, Seattle, WA, USA.

Nucleic Acids Research
|May 9, 2007
PubMed
Summary

SCOPE is a new tool that identifies gene regulatory motifs without needing adjustable parameters. It accurately finds potential regulatory elements in gene sets, offering an intuitive web server for biologists.

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Area of Science:

  • Bioinformatics
  • Computational Biology
  • Genomics

Background:

  • Identifying regulatory motifs is crucial for understanding gene regulation.
  • Existing motif-finding tools often require parameter tuning, limiting accessibility.

Purpose of the Study:

  • To develop and present SCOPE, a novel, parameter-free method for de novo identification of regulatory motifs.
  • To provide an accessible web server for motif discovery.

Main Methods:

  • SCOPE employs an ensemble learning approach, combining outputs from three specialized motif-finding algorithms.
  • It processes gene sets using gene names or FASTA sequences across various species.

Main Results:

  • SCOPE demonstrated significantly higher accuracy in motif identification compared to other web-based tools.
  • The parameter-free nature results in an intuitive user interface.
  • Results are presented graphically with detailed information available upon request.

Conclusions:

  • SCOPE offers an efficient and accurate solution for regulatory motif discovery.
  • The accessible web server empowers biologists with advanced motif identification capabilities.
  • Its performance favorably compares to existing motif finders.