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

Comparing Copy Number Variations and SNPs02:26

Comparing Copy Number Variations and SNPs

17.9K
Sequencing of the human genome has opened up several best-kept secrets of the genome. Scientists have identified thousands of genome variations that exist within a population. These variations can be a single nucleotide or a larger chromosomal variation.
Copy number variations or CNVs are the structural variations that cover more than 1kb of DNA sequence. The single nucleotide polymorphism (SNP), on the other hand, is a single nucleotide change or a point mutation that is found in more than 1%...
17.9K
Base-pairing and DNA Repair02:27

Base-pairing and DNA Repair

65.0K
65.0K
Single Nucleotide Polymorphisms-SNPs01:05

Single Nucleotide Polymorphisms-SNPs

15.6K
A single nucleotide polymorphism or SNP is a single nucleotide variation at a specific genomic position in a large population. It is the most prevalent type of sequence variation found in the human genome. Point mutations that occur in more than 1% of the population qualify as SNPs. These are present once every 1000 nucleotides on an average in the human genome. Replacement of a purine with another purine (A/G) or a pyrimidine with another pyrimidine (C/T) is known as a transition. In contrast,...
15.6K

You might also read

Related Articles

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

Sort by
Same author

Expanded clinical and genetic characterization of autosomal recessive HMGCR-related muscular dystrophy.

Journal of neuromuscular diseases·2026
Same author

Consanguinity in the Lebanese population: knowledge, attitudes and practices.

Journal of community genetics·2026
Same author

Blended Phenotypes in Siblings: Dual Diagnoses of Nicolaides-Baraitser and Craniosynostosis Syndromes.

Molecular syndromology·2025
Same author

Clinical and molecular findings in actin-related inborn errors of immunity: the middle East and North Africa registry.

Frontiers in genetics·2025
Same author

Recurrent nonsense p.Trp3416* variant in the <i>DMD</i> gene identified in healthy Lebanese individuals: Implications for variant classification and genotype-phenotype correlations.

Journal of neuromuscular diseases·2025
Same author

Co-Occurrence of Variants in 3 Genes in a Patient with Congenital Skeletal Dysplasia and Cardiac Anomalies: Diagnostic Challenge Posed by a Blended Phenotype.

Molecular syndromology·2025

Related Experiment Video

Updated: Aug 25, 2025

Detection of Rare Mutations in CtDNA Using Next Generation Sequencing
11:11

Detection of Rare Mutations in CtDNA Using Next Generation Sequencing

Published on: August 24, 2017

16.9K

New complementary python codes to locate Single Nucleotide Polymorphisms (SNPs) and Overlapping G-Quadruplex

Mona Saad1, Marc Shebaby2, Cybel Mehawej3

  • 1Gilbert and Rose-Marie Chagoury School of Medicine, Lebanese American University, Byblos, Lebanon.

Methodsx
|October 17, 2022
PubMed
Summary

We developed computational tools to identify overlaps between genetic variations called single nucleotide polymorphisms (SNPs) and G-quadruplexes (G4s) DNA structures, aiding in understanding gene regulation. These tools accurately mapped most tested SNPs to nearby G4 sequences.

Keywords:
G-quadruplexes (G4s)Overlapping G4sPythonSingle nucleotide polymorphisms (SNPs)

More Related Videos

Single-Molecule Fluorescence Visualization of DNA Polymerase Dynamics at G-Quadruplexes
05:37

Single-Molecule Fluorescence Visualization of DNA Polymerase Dynamics at G-Quadruplexes

Published on: April 4, 2025

816
Novel Sequence Discovery by Subtractive Genomics
09:40

Novel Sequence Discovery by Subtractive Genomics

Published on: January 25, 2019

8.7K

Related Experiment Videos

Last Updated: Aug 25, 2025

Detection of Rare Mutations in CtDNA Using Next Generation Sequencing
11:11

Detection of Rare Mutations in CtDNA Using Next Generation Sequencing

Published on: August 24, 2017

16.9K
Single-Molecule Fluorescence Visualization of DNA Polymerase Dynamics at G-Quadruplexes
05:37

Single-Molecule Fluorescence Visualization of DNA Polymerase Dynamics at G-Quadruplexes

Published on: April 4, 2025

816
Novel Sequence Discovery by Subtractive Genomics
09:40

Novel Sequence Discovery by Subtractive Genomics

Published on: January 25, 2019

8.7K

Area of Science:

  • Genomics
  • Bioinformatics
  • Molecular Biology

Background:

  • G-quadruplexes (G4s) are non-canonical DNA secondary structures crucial for gene regulation.
  • Single nucleotide polymorphisms (SNPs) are common genetic variations that can influence individual traits and disease susceptibility.
  • SNPs located within G4 sequences have the potential to alter gene regulation.

Purpose of the Study:

  • To develop computational tools for identifying overlaps between predicted G4 sequences and SNPs.
  • To map genetic variants to their closest or overlapping G4 structures.
  • To provide a method for investigating the functional impact of SNPs on G4-mediated gene regulation.

Main Methods:

  • Development of two Python-based computational codes: SNP-locator and G4-overlap.
  • SNP-locator identifies SNP positions within genomic regions (promoters, regulatory regions, exons, introns) using FASTA sequences and genetic variant nomenclature.
  • G4-overlap maps identified SNPs to overlapping or adjacent G4 sequences.

Main Results:

  • The developed computational tools (SNP-locator and G4-overlap) were validated on 31 SNP variants in cytochrome P450 and podocyte-marker genes.
  • Out of 31 tested SNPs, 28 were accurately located by the codes.
  • The tools successfully mapped SNPs to overlapping or the closest G4 sequences.

Conclusions:

  • The developed SNP-locator and G4-overlap codes are effective for identifying the relationship between SNPs and G4 sequences.
  • These computational tools facilitate the study of how genetic variations within G4 structures impact gene regulation.
  • The accurate mapping of SNPs to G4s provides a foundation for further research into SNP-associated diseases and personalized medicine.