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

Conserved Binding Sites01:49

Conserved Binding Sites

5.3K
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...
5.3K
Protein Families02:47

Protein Families

17.5K
Protein families are groups of homologous proteins; that is, they have similarities in amino acid sequences and three-dimensional structures. Protein families usually occur because of gene duplication, where an additional copy of a gene is inserted into the genome of an organism.   Mutations that change the amino acids but still allow the protein to be properly synthesized, will lead to new protein family members.   If these new proteins contain similar amino acids in key...
17.5K
Modern Molecular Taxonomy01:29

Modern Molecular Taxonomy

839
Advancements in molecular biology have revolutionized the identification and characterization of bacteria, with multiple methods leveraging DNA sequencing for enhanced precision. As sequencing technologies improve and costs decline, these approaches are increasingly used in clinical, environmental, and evolutionary studies.Multilocus Sequence Typing (MLST) examines several housekeeping genes, essential chromosomal genes encoding cellular functions, to distinguish strains. Approximately...
839
Conservation of Protein Domains Over Different Proteins02:26

Conservation of Protein Domains Over Different Proteins

15.0K
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.
A limited set of protein domains often duplicate and recombine during evolution. These domains can be organized in different combinations to...
15.0K
Nucleic Acid Structure01:25

Nucleic Acid Structure

10.3K
The pentose sugar in DNA is deoxyribose, while in RNA the pentose sugar is ribose. The difference between the sugars is the presence of the hydroxyl group on the ribose's second carbon and a hydrogen on the deoxyribose's second carbon. The phosphate residue attaches to the hydroxyl group of the 5′ carbon of one sugar and the hydroxyl group of the 3′ carbon of the sugar of the next nucleotide, which forms  a 5′ to 3′ phosphodiester linkage.
DNA Structure
DNA...
10.3K
DNA Microarrays02:34

DNA Microarrays

23.0K
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...
23.0K

You might also read

Related Articles

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

Sort by
Same author

Autoregulation of three yeast ribosomal protein genes by splicing inhibition.

G3 (Bethesda, Md.)·2026
Same author

Autoregulation of RPL7B by inhibition of a structural splicing enhancer.

Nucleic acids research·2025
Same author

Autoregulation of <i>RPL7B</i> by inhibition of a structural splicing enhancer.

bioRxiv : the preprint server for biology·2025
Same author

Aberrant homeodomain-DNA cooperative dimerization underlies distinct developmental defects in two dominant <i>CRX</i> retinopathy models.

Genome research·2024
Same author

Aberrant homeodomain-DNA cooperative dimerization underlies distinct developmental defects in two dominant <i>CRX</i> retinopathy models.

bioRxiv : the preprint server for biology·2024
Same author

Finding motifs using DNA images derived from sparse representations.

Bioinformatics (Oxford, England)·2023
Same journal

Protein Sequence Analysis Using the MPI Bioinformatics Toolkit.

Current protocols in bioinformatics·2020
Same journal

Exploring Manually Curated Annotations of Intrinsically Disordered Proteins with DisProt.

Current protocols in bioinformatics·2020
Same journal

Network Building with the Cytoscape BioGateway App Explained in Five Use Cases.

Current protocols in bioinformatics·2020
Same journal

Expanding the Perseus Software for Omics Data Analysis With Custom Plugins.

Current protocols in bioinformatics·2020
Same journal

Exploring Non-Coding RNAs in RNAcentral.

Current protocols in bioinformatics·2020
Same journal

How to Illuminate the Dark Proteome Using the Multi-omic OpenProt Resource.

Current protocols in bioinformatics·2020
See all related articles

Related Experiment Video

Updated: Apr 4, 2026

Analyzing and Building Nucleic Acid Structures with 3DNA
16:24

Analyzing and Building Nucleic Acid Structures with 3DNA

Published on: April 26, 2013

21.4K

DNA Motif Databases and Their Uses.

Gary D Stormo1

  • 1Washington University School of Medicine, St. Louis, Missouri.

Current Protocols in Bioinformatics
|September 4, 2015
PubMed
Summary
This summary is machine-generated.

Transcription factors (TFs) bind specific DNA sequences, often represented by position weight matrices (PWMs). This overview covers common TF motif databases and their applications in biological research.

Keywords:
DNA motifsbinding site predictionsposition weight matricestranscription factors

More Related Videos

Author Spotlight: Advancements in DNA Nanosensors &#8211; Addressing Sensitivity and Selectivity Challenges in Molecular Detection
07:16

Author Spotlight: Advancements in DNA Nanosensors – Addressing Sensitivity and Selectivity Challenges in Molecular Detection

Published on: February 9, 2024

1.7K
In Vivo Functional Study of Disease-associated Rare Human Variants Using Drosophila
06:41

In Vivo Functional Study of Disease-associated Rare Human Variants Using Drosophila

Published on: August 20, 2019

14.5K

Related Experiment Videos

Last Updated: Apr 4, 2026

Analyzing and Building Nucleic Acid Structures with 3DNA
16:24

Analyzing and Building Nucleic Acid Structures with 3DNA

Published on: April 26, 2013

21.4K
Author Spotlight: Advancements in DNA Nanosensors &#8211; Addressing Sensitivity and Selectivity Challenges in Molecular Detection
07:16

Author Spotlight: Advancements in DNA Nanosensors – Addressing Sensitivity and Selectivity Challenges in Molecular Detection

Published on: February 9, 2024

1.7K
In Vivo Functional Study of Disease-associated Rare Human Variants Using Drosophila
06:41

In Vivo Functional Study of Disease-associated Rare Human Variants Using Drosophila

Published on: August 20, 2019

14.5K

Area of Science:

  • Genomics
  • Bioinformatics
  • Molecular Biology

Background:

  • Transcription factors (TFs) are proteins that control gene expression by binding to specific DNA sequences.
  • The DNA-binding specificity of a TF is commonly represented using a position weight matrix (PWM).
  • Numerous databases catalog these DNA motifs, serving as crucial resources in biological research.

Purpose of the Study:

  • To provide an overview of position weight matrices (PWMs) for representing TF-DNA binding specificity.
  • To describe commonly used databases for DNA motifs.
  • To highlight typical applications of TF motif analysis in biological research.

Main Methods:

  • Literature review of TF motif databases and their applications.
  • Description of the concept and representation of TF-DNA binding specificity using PWMs.

Main Results:

  • Identification and description of key PWM concepts.
  • Compilation of frequently utilized DNA motif databases.
  • Examples of common biological questions addressed using motif analysis.

Conclusions:

  • PWMs are a standard method for characterizing TF binding specificity.
  • Motif databases are essential tools for exploring gene regulation and other biological questions.
  • Understanding TF-DNA interactions through motif analysis facilitates advancements in various biological research areas.