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Updated: Jun 13, 2026
09:37
An Integrated Approach for Microprotein Identification and Sequence Analysis
Published on: July 12, 2022
Phyloscan: locating transcription-regulating binding sites in mixed aligned and unaligned sequence data.
Michael J Palumbo1, Lee A Newberg
1Wadsworth Center, New York State Department of Health, Empire State Plaza, P.O. Box 509, Albany, NY 12201-0509, USA.
Nucleic Acids Research
|May 4, 2010
Summary
Phyloscan identifies functional transcription factor binding sites by analyzing evolutionary conservation and site frequency. This computational tool improves accuracy in finding gene regulatory elements, reducing false positives in DNA sequence analysis.
Area of Science:
- Genetics
- Bioinformatics
- Molecular Biology
Background:
- Gene expression regulation is crucial, with transcription factors binding to DNA promoter regions.
- Identifying these transcription factor binding sites computationally is challenging due to short, variable motifs.
- Existing methods often yield many false positives, missing true functional sites.
Purpose of the Study:
- To develop a computational tool, Phyloscan, to accurately identify functional transcription factor binding sites.
- To overcome limitations of existing methods in distinguishing functional sites from non-functional sequences.
- To provide a free, accessible web resource for researchers.
Main Methods:
- Phyloscan exploits evolutionary conservation of functional binding sites.
- It also utilizes the tendency for functional sites to occur multiple times in promoter regions.
- The tool scans DNA sequences for these conserved, recurring patterns.
Main Results:
- Phyloscan effectively distinguishes functional binding sites from non-functional DNA sequences.
- The method significantly reduces false positives compared to other computational approaches.
- It successfully identifies experimentally verified binding sites.
Conclusions:
- Phyloscan offers an improved computational method for identifying transcription factor binding sites.
- The tool enhances the accuracy of DNA sequence analysis in gene regulation studies.
- The Phyloscan website provides a valuable, free resource for the scientific community.
Related Concept Videos
01:49Conserved Binding Sites
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Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally analyses the...
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally analyses the...
02:54Evolutionary Relationships through Genome Comparisons
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02:02Cis-regulatory Sequences
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...
02:02Cis-regulatory Sequences
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02:05Gene Evolution - Fast or Slow?
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In contrast, regions which code...
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