Jove
Visualize
Contact Us
JoVE
x logofacebook logolinkedin logoyoutube logo
ABOUT JoVE
OverviewLeadershipBlogJoVE Help Center
AUTHORS
Publishing ProcessEditorial BoardScope & PoliciesPeer ReviewFAQSubmit
LIBRARIANS
TestimonialsSubscriptionsAccessResourcesLibrary Advisory BoardFAQ
RESEARCH
JoVE JournalMethods CollectionsJoVE Encyclopedia of ExperimentsArchive
EDUCATION
JoVE CoreJoVE BusinessJoVE Science EducationJoVE Lab ManualFaculty Resource CenterFaculty Site
Terms & Conditions of Use
Privacy Policy
Policies

Related Concept Videos

DNA Microarrays02:34

DNA Microarrays

Microarrays are high-throughput and relatively inexpensive assays that can be automated to analyze large quantities of data at a time. They are used in genome-wide studies to compare gene or protein expression under two varied conditions, such as healthy and diseased states. Microarrays consist of glass or silica slides on which probe molecules are covalently attached through surface functionalization. Most commonly, the slides are prepared through the chemisorption of silanes to silica...
DNA Topoisomerases02:02

DNA Topoisomerases

Topoisomerases are enzymes that relax overwound DNA molecules during various cell processes, including DNA replication and transcription. These enzymes regulate positive and negative DNA supercoiling without changing the nucleotide sequence. DNA overwinding in a clockwise direction results in positively supercoiled DNA, whereas underwinding in a counterclockwise direction produces negatively supercoiled DNA.
Types and Mechanism of action
Topoisomerases are divided into two main types.  Type I...
Evolutionary Relationships through Genome Comparisons02:54

Evolutionary Relationships through Genome Comparisons

Genome comparison is one of the excellent ways to interpret the evolutionary relationships between organisms. The basic principle of genome comparison is that if two species share a common feature, it is likely encoded by the DNA sequence conserved between both species. The advent of genome sequencing technologies in the late 20th century enabled scientists to understand the concept of conservation of domains between species and helped them to deduce evolutionary relationships across diverse...

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by
Same author

Novel Mannich based derivatives of isoliquiritigenin and liquiritigenin, bioactive constituents of <i>Glycyrrhiza glabra</i>, as potent antimalarial agents.

Natural product research·2026
Same author

Molecular Interactions of Precocene Derivatives in Crystal Structures and in Silico Evaluation of Their Binding to Estrogen Receptors.

Chemistry, an Asian journal·2026
Same author

Apoptosis Induction, Disruption of Cytoskeleton Remodeling and EMT Inhibition as Major Mechanism(s) Underlying the Pleiotropic Action of Withania somnifera in Breast Cancer.

Cytoskeleton (Hoboken, N.J.)·2026
Same author

Deciphering diabetes-related genetic markers using <i>in silico</i> methods: insights into <i>Gymnema sylvestre</i>'s therapeutic role for diabetes mellitus.

In silico pharmacology·2026
Same author

Comparison of Tylophora indica with Tylophora pauciflora coupled with network pharmacology of phenanthroindolizidine alkaloids sheds light on its antiallergic potential.

Molecular biology reports·2026
Same author

Vasorelaxation and antihypertensive activity of standardized extract of Gymnema sylvestre in rodent model.

Fitoterapia·2026

Related Experiment Video

Updated: Jun 25, 2026

DNA-affinity-purified Chip (DAP-chip) Method to Determine Gene Targets for Bacterial Two component Regulatory Systems
12:24

DNA-affinity-purified Chip (DAP-chip) Method to Determine Gene Targets for Bacterial Two component Regulatory Systems

Published on: July 21, 2014

Performance evaluation of DNA motif discovery programs.

Chandra Prakash Singh1, Feroz Khan, Bhartendu Nath Mishra

  • 1Department of Computer Sciences, R.S.M.T., U.P. College, Varanasi, India. chand_11_2000@yahoo.com

Bioinformation
|March 4, 2009
PubMed
Summary

Identifying transcription factor binding sites is key for understanding genetic networks. Our study benchmarks web tools, finding low accuracy for nucleotide and binding site predictions, but high accuracy for activator binding sites.

Keywords:
DNA binding siteaccuracyevaluationmotif discoveryregulatory proteins

More Related Videos

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

Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues
07:08

Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues

Published on: July 14, 2015

Related Experiment Videos

Last Updated: Jun 25, 2026

DNA-affinity-purified Chip (DAP-chip) Method to Determine Gene Targets for Bacterial Two component Regulatory Systems
12:24

DNA-affinity-purified Chip (DAP-chip) Method to Determine Gene Targets for Bacterial Two component Regulatory Systems

Published on: July 21, 2014

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

Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues
07:08

Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues

Published on: July 14, 2015

Area of Science:

  • Genomics
  • Bioinformatics
  • Molecular Biology

Background:

  • Transcription factor binding site identification is crucial for understanding gene regulation.
  • Existing web tools for motif discovery have not been comprehensively evaluated.
  • Deciphering genetic regulatory networks relies on accurate identification of these binding sites.

Purpose of the Study:

  • To benchmark the performance of sequence-based motif discovery tools.
  • To evaluate the strengths and weaknesses of available web tools for identifying transcription factor binding sites.
  • To provide a comprehensive set of performance measures for tool evaluation.

Main Methods:

  • Developed a comprehensive set of performance measures.
  • Utilized large-scale datasets from the Escherichia coli genome and the RegulonDB database.
  • Benchmarked sequence-based motif discovery tools.

Main Results:

  • Nucleotide-based prediction accuracy was generally low.
  • Binding site-based prediction accuracy was often low.
  • Activator binding site-based prediction accuracy was found to be high.

Conclusions:

  • The performance of sequence-based motif discovery tools varies significantly.
  • Current tools show limitations in accurately predicting general binding sites and nucleotide patterns.
  • Activator binding site prediction demonstrates higher accuracy, suggesting potential for focused applications.