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

Improving Translational Accuracy02:07

Improving Translational Accuracy

11.8K
Base complementarity between the three base pairs of mRNA codon and the tRNA anticodon is not a failsafe mechanism. Inaccuracies can range from a single mismatch to no correct base pairing at all. The free energy difference between the correct and nearly correct base pairs can be as small as 3 kcal/ mol. With complementarity being the only proofreading step, the estimated error frequency would be one wrong amino acid in every 100 amino acids incorporated. However, error frequencies observed in...
11.8K
Sanger Sequencing01:57

Sanger Sequencing

756.0K
DNA sequencing is a fundamental technique that is routinely used in the biological sciences. This method can be applied to a range of questions at different scales - from the sequencing of a cloned DNA fragment or the study of a mutation in a gene up to whole-genome sequencing. However, despite the widespread use of sequencing today, it was not until 1977 that Fredrick Sanger and his collaborators developed the chain-termination method to decode DNA sequences. It relies on the separation of a...
756.0K
¹H NMR: Long-Range Coupling01:27

¹H NMR: Long-Range Coupling

1.9K
The coupling interactions of nuclei across four or more bonds are usually weak, with J values less than 1 Hz. While these are usually not observed in spectra, the presence of multiple bonds along the coupling pathway can result in observable long-range coupling.
In alkenes, spin information is communicated via σ–π overlap, as seen in allylic (four-bond) and homoallylic (five-bond) couplings. These coupling interactions are stronger when the σ bond is parallel to the alkene...
1.9K
Maxam-Gilbert Sequencing01:05

Maxam-Gilbert Sequencing

11.4K
In the same year as the discovery of the Sanger sequencing method, another group of scientists, Allan Maxam and Walter Gilbert, demonstrated their chemical-cleavage method for DNA sequencing. The Maxam-Gilbert method relies on using different chemicals that can cleave the DNA sequence at specific sites, the separation of resulting DNA fragments of variable size using electrophoresis, and deciphering the DNA sequence from the resulting gel bands.
Challenges of the Maxam-Gilbert Method
The...
11.4K
Multi-species Conserved Sequences02:51

Multi-species Conserved Sequences

4.0K
Next-generation sequencing technologies have created large genomic databases of a variety of animals and plants. Ever since the human genome project was completed, scientists studied the genome of primates, mammals, and other phylogenetically distant living beings. Such large-scale  studies have provided new insights into the evolutionary relationship between organisms.
Although the genome of each species varies greatly from each other, a few sequences are highly conserved. Such conserved...
4.0K
Conservative Site-specific Recombination and Phase Variation02:53

Conservative Site-specific Recombination and Phase Variation

6.1K
Because the DNA segments are cut and reorganized in a direction-specific manner, site-specific recombination has emerged as an efficient genetic engineering technique. Flippase and Cyclization recombinases or Flp and Cre, respectively, are two members of the tyrosine recombinase family derived from bacteriophages, that are used to mediate site-specific DNA insertions, deletions, and targeted expression of proteins in mammalian cell lines.
The recognition sites for Cre recombinase called LoxP...
6.1K

You might also read

Related Articles

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

Sort by
Same author

The Effect of Nephrology Referral on CKD Outcomes in Israel.

Clinical journal of the American Society of Nephrology : CJASN·2026
Same author

Demography-dependent variability in the human tumor mycobiome.

Microbiology spectrum·2026
Same author

Molecular Systems Biology at 20: reflecting on the past, envisioning the future.

Molecular systems biology·2025
Same author

Transcriptional programs of cell identity and p53-induced stress responses are associated with distinctive features of spatial genome organization.

Nucleic acids research·2025
Same author

A reference model of circulating hematopoietic stem cells across the lifespan with applications to diagnostics.

Nature medicine·2025
Same author

4CAC: 4-class classifier of metagenome contigs using machine learning and assembly graphs.

Nucleic acids research·2024
Same journal

DeepMethylation: A deep learning framework for tissue-specific DNA methylation prediction and functional variant annotation.

PLoS computational biology·2026
Same journal

Redefining and estimating the early-phase reproduction ratio for epidemic outbreaks in spatially structured populations.

PLoS computational biology·2026
Same journal

Optimized phenotype definitions boost GWAS power.

PLoS computational biology·2026
Same journal

Detection, communication, and individual identification with deep audio embeddings: A case study with North Atlantic right whales.

PLoS computational biology·2026
Same journal

Exploring the structural lexicon of the Proteome via Metric Geometry.

PLoS computational biology·2026
Same journal

Linking retinal sampling in neural encoding models to temporal profiles of visual processing in humans.

PLoS computational biology·2026
See all related articles

Related Experiment Video

Updated: Aug 23, 2025

Ultra-long Read Sequencing for Whole Genomic DNA Analysis
10:34

Ultra-long Read Sequencing for Whole Genomic DNA Analysis

Published on: March 15, 2019

23.0K

Parameterized syncmer schemes improve long-read mapping.

Abhinav Dutta1, David Pellow2, Ron Shamir2

  • 1Computer Science and Engineering, Indian Institute of Technology Patna, Patna, India.

Plos Computational Biology
|October 28, 2022
PubMed
Summary
This summary is machine-generated.

Parameterized syncmer schemes (PSS) improve long-read mapping by reducing unmapped reads by 20-60% and increasing accuracy, especially at low sequence identity. This novel method enhances genome analysis in challenging scenarios like cancer research.

More Related Videos

Targeted DNA Methylation Analysis by Next-generation Sequencing
08:38

Targeted DNA Methylation Analysis by Next-generation Sequencing

Published on: February 24, 2015

37.3K
Simultaneous Mapping and Quantitation of Ribonucleotides in Human Mitochondrial DNA
12:35

Simultaneous Mapping and Quantitation of Ribonucleotides in Human Mitochondrial DNA

Published on: November 14, 2017

9.5K

Related Experiment Videos

Last Updated: Aug 23, 2025

Ultra-long Read Sequencing for Whole Genomic DNA Analysis
10:34

Ultra-long Read Sequencing for Whole Genomic DNA Analysis

Published on: March 15, 2019

23.0K
Targeted DNA Methylation Analysis by Next-generation Sequencing
08:38

Targeted DNA Methylation Analysis by Next-generation Sequencing

Published on: February 24, 2015

37.3K
Simultaneous Mapping and Quantitation of Ribonucleotides in Human Mitochondrial DNA
12:35

Simultaneous Mapping and Quantitation of Ribonucleotides in Human Mitochondrial DNA

Published on: November 14, 2017

9.5K

Area of Science:

  • Bioinformatics
  • Computational Biology
  • Genomics

Background:

  • Long-read sequencing presents mapping challenges due to low sequence similarity caused by high error and mutation rates.
  • Minimizers are a common sequence sketching method for mapping, but are sensitive to errors.
  • Syncmers offer improved robustness to errors and mutations compared to minimizers.

Purpose of the Study:

  • To introduce Parameterized Syncmer Schemes (PSS) as a generalization of syncmers for improved long-read mapping.
  • To provide theoretical analysis for multi-parameter PSS and demonstrate their combination with downsampling or minimizers.
  • To evaluate the performance of PSS-based mapping algorithms in comparison to existing methods.

Main Methods:

  • Developed and theoretically analyzed Parameterized Syncmer Schemes (PSS).
  • Integrated PSS into existing mappers, specifically minimap2 and Winnowmap2.
  • Conducted tests on simulated and real long-read data across various genomes.

Main Results:

  • PSS-based algorithms reduced unmapped reads by 20-60% at high compression with lower memory usage.
  • Performance gains were more significant at lower sequence identities, with PSS-minimap showing 63% fewer unmapped reads at 75% identity.
  • PSS-based mapping demonstrated higher accuracy, with 8% fewer incorrectly mapped reads in PSS-minimap at 75% identity.
  • PSS consistently outperformed original minimizer and syncmer schemes across various compression and error rates.

Conclusions:

  • Parameterized Syncmer Schemes (PSS) offer a significant improvement for long-read mapping, particularly in error-prone or divergent genomic data.
  • PSS provide a flexible framework to achieve desired compression and window guarantees, enhancing mapping accuracy and efficiency.
  • The implementation and validation of PSS in popular mappers demonstrate their practical utility and broad applicability in genomic analyses.