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Related Concept Videos

Conserved Binding Sites01:49

Conserved Binding Sites

Many proteins’ biological role depends on their interactions with their ligands, small molecules that bind to specific locations on the protein known as ligand-binding sites. Ligand-binding sites are often conserved among homologous proteins as these sites are critical for protein function.
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...
Conserved Binding Sites01:49

Conserved Binding Sites

Many proteins’ biological role depends on their interactions with their ligands, small molecules that bind to specific locations on the protein known as ligand-binding sites. Ligand-binding sites are often conserved among homologous proteins as these sites are critical for protein function.
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...
Transcription Factors02:16

Transcription Factors

Tissue-specific transcription factors contribute to diverse cellular functions in mammals. For example, the gene for beta globin, a major component of hemoglobin, is present in all cells of the body. However, it is only expressed in red blood cells because the transcription factors that can bind to the promoter sequences of the beta globin gene are only expressed in these cells. Tissue-specific transcription factors also ensure that mutations in these factors may impair only the function of...
Transcription Factors02:16

Transcription Factors

Tissue-specific transcription factors contribute to diverse cellular functions in mammals. For example, the gene for beta globin, a major component of hemoglobin, is present in all cells of the body. However, it is only expressed in red blood cells because the transcription factors that can bind to the promoter sequences of the beta globin gene are only expressed in these cells. Tissue-specific transcription factors also ensure that mutations in these factors may impair only the function of...
Cooperative Binding of Transcription Regulators02:13

Cooperative Binding of Transcription Regulators

Transcriptional regulators bind to specific cis-regulatory sequences in the DNA to regulate gene transcription. These cis-regulatory sequences are very short, usually less than ten nucleotide pairs in length. The short length means that there is a high probability of the exact same sequence randomly occurring throughout the genome.  Since regulators can also bind to groups of similar sequences, this further increases the chances of random binding. Transcriptional regulators form dimers that...
Cooperative Binding of Transcription Regulators02:13

Cooperative Binding of Transcription Regulators

Transcriptional regulators bind to specific cis-regulatory sequences in the DNA to regulate gene transcription. These cis-regulatory sequences are very short, usually less than ten nucleotide pairs in length. The short length means that there is a high probability of the exact same sequence randomly occurring throughout the genome.  Since regulators can also bind to groups of similar sequences, this further increases the chances of random binding. Transcriptional regulators form dimers that...

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Related Experiment Video

Updated: Jun 25, 2026

High Sensitivity Measurement of Transcription Factor-DNA Binding Affinities by Competitive Titration Using Fluorescence Microscopy
06:38

High Sensitivity Measurement of Transcription Factor-DNA Binding Affinities by Competitive Titration Using Fluorescence Microscopy

Published on: February 7, 2019

COTRASIF: conservation-aided transcription-factor-binding site finder.

Bogdan Tokovenko1, Rostyslav Golda, Oleksiy Protas

  • 1Department of Genetic Information Translation Mechanisms, Institute of Molecular Biology and Genetics, NAS of Ukraine. to.bogdan@gmail.com

Nucleic Acids Research
|March 7, 2009
PubMed
Summary

COTRASIF is a web tool for identifying evolutionary conserved regulatory regions, specifically transcription factor-binding sites (TFBS), across genomes. It enhances accuracy by filtering predictions based on evolutionary conservation in related species.

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Related Experiment Videos

Last Updated: Jun 25, 2026

High Sensitivity Measurement of Transcription Factor-DNA Binding Affinities by Competitive Titration Using Fluorescence Microscopy
06:38

High Sensitivity Measurement of Transcription Factor-DNA Binding Affinities by Competitive Titration Using Fluorescence Microscopy

Published on: February 7, 2019

Determination of Tripartite Interaction between Two Monomers of a MADS-box Transcription Factor and a Calcium Sensor Protein by BiFC-FRET-FLIM Assay
14:34

Determination of Tripartite Interaction between Two Monomers of a MADS-box Transcription Factor and a Calcium Sensor Protein by BiFC-FRET-FLIM Assay

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Enhanced Yeast One-hybrid Screens To Identify Transcription Factor Binding To Human DNA Sequences
11:25

Enhanced Yeast One-hybrid Screens To Identify Transcription Factor Binding To Human DNA Sequences

Published on: February 11, 2019

Area of Science:

  • Genomics
  • Bioinformatics
  • Computational Biology

Background:

  • Identifying functional regulatory elements in eukaryotic genomes is crucial for understanding gene regulation.
  • Transcription factor-binding sites (TFBS) are key regulatory regions, but their accurate, genome-wide identification remains challenging.
  • Existing methods often struggle with high false-positive rates and integrating diverse data sources.

Purpose of the Study:

  • To present COTRASIF, a novel web-based tool for the genome-wide search of evolutionary conserved regulatory regions (TFBS) in eukaryotic gene promoters.
  • To provide an integrated solution combining promoter databases and TFBS matrices with an evolutionary conservation filter.
  • To improve the accuracy and efficiency of TFBS prediction.

Main Methods:

  • COTRASIF utilizes a web-based platform for genome-wide TFBS searching in eukaryotic gene promoters.
  • Prediction methods include position-weight matrix and hidden Markov models, leveraging JASPAR and TRANSFAC databases.
  • An integrated evolutionary conservation filter selects TFBS present in orthologous genes across related species to reduce false positives.

Main Results:

  • COTRASIF offers a fully integrated solution with an updated promoter database and TFBS matrices.
  • The tool implements an evolutionary conservation filter to enhance prediction specificity.
  • It provides a user-friendly interface for powerful, genome-wide TFBS searching.

Conclusions:

  • COTRASIF is a powerful and easy-to-use web tool for accurate, genome-wide TFBS identification.
  • The integration of evolutionary conservation significantly reduces false positives in TFBS predictions.
  • COTRASIF represents a valuable resource for researchers studying gene regulation and eukaryotic genomics.