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

Mismatch Repair01:36

Mismatch Repair

44.9K
Overview
44.9K
Mismatch Repair01:20

Mismatch Repair

7.0K
Organisms are capable of detecting and fixing nucleotide mismatches that occur during DNA replication. This sophisticated process requires identifying the new strand and replacing the erroneous bases with correct nucleotides. Mismatch repair is coordinated by many proteins in both prokaryotes and eukaryotes.
The Mutator Protein Family Plays a Key Role in DNA Mismatch Repair
The human genome has more than 3 billion base pairs of DNA per cell. Prior to cell division, that vast amount of genetic...
7.0K
Mismatch Repair01:36

Mismatch Repair

12.3K
12.3K
Maxam-Gilbert Sequencing01:05

Maxam-Gilbert Sequencing

13.6K
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...
13.6K
Sign Test for Matched Pairs01:17

Sign Test for Matched Pairs

457
The sign test for matched pairs offers a robust method for comparing two paired samples, often for the effects of an intervention in one of them. This method is very useful in situations where the underlying distribution of the data is unknown. The test compares two related samples—often pre- and post-treatment measurements on the same subjects—to determine if there are significant differences in their median values.
To conduct the sign test, we first calculate the differences in...
457
Predicting Products: Substitution vs. Elimination02:52

Predicting Products: Substitution vs. Elimination

15.1K
When a nucleophile and an alkyl halide react, nucleophilic substitution and β-elimination reactions compete to generate products.
The following factors can influence the mechanisms competing against each other:
15.1K

You might also read

Related Articles

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

Sort by
Same author

<i>Special Section:</i> 12th International Computational Advances in Bio and Medical Sciences (ICCABS 2023).

Journal of computational biology : a journal of computational molecular cell biology·2025
Same author

Disambiguating a Soft Metagenomic Clustering.

Journal of computational biology : a journal of computational molecular cell biology·2025
Same author

SCEMENT: scalable and memory efficient integration of large-scale single-cell RNA-sequencing data.

Bioinformatics (Oxford, England)·2025
Same author

GraphSlimmer: Preserving Read Mappability with the Minimum Number of Variants.

Journal of computational biology : a journal of computational molecular cell biology·2024
Same author

MCPNet: a parallel maximum capacity-based genome-scale gene network construction framework.

Bioinformatics (Oxford, England)·2023
Same author

On the Hardness of Sequence Alignment on De Bruijn Graphs.

Journal of computational biology : a journal of computational molecular cell biology·2022
Same journal

GMSA: A Graph Matching and Point Cloud Registration-Based Method for Spatial Transcriptomics Data Alignment.

Journal of computational biology : a journal of computational molecular cell biology·2026
Same journal

Investigations on Multiple Protein Scaffold Filling.

Journal of computational biology : a journal of computational molecular cell biology·2026
Same journal

Cell Type Prediction for Single-Cell RNA Sequencing Utilizing Unsupervised Domain Adaptation and Semi-Supervised Learning.

Journal of computational biology : a journal of computational molecular cell biology·2026
Same journal

PPIGAN: Prediction of Protein-Protein Interactions Using Generative Adversarial Networks.

Journal of computational biology : a journal of computational molecular cell biology·2026
Same journal

Deep Structure-Enhanced Cell Clustering Model for Single-Cell RNA Sequencing Data.

Journal of computational biology : a journal of computational molecular cell biology·2026
Same journal

Asymmetric Drug-Drug Interaction Prediction Based on Generative Adversarial Networks and Knowledge Graph.

Journal of computational biology : a journal of computational molecular cell biology·2026
See all related articles

Related Experiment Video

Updated: Mar 22, 2026

Proofreading and DNA Repair Assay Using Single Nucleotide Extension and MALDI-TOF Mass Spectrometry Analysis
11:08

Proofreading and DNA Repair Assay Using Single Nucleotide Extension and MALDI-TOF Mass Spectrometry Analysis

Published on: June 19, 2018

10.3K

A Provably Efficient Algorithm for the k-Mismatch Average Common Substring Problem.

Sharma V Thankachan1, Alberto Apostolico1, Srinivas Aluru1

  • 1College of Computing, Georgia Institute of Technology , Atlanta, Georgia .

Journal of Computational Biology : a Journal of Computational Molecular Cell Biology
|April 9, 2016
PubMed
Summary
This summary is machine-generated.

This study introduces an efficient algorithm for comparing biological sequences with mismatches, improving upon existing methods for applications like genome analysis and evolutionary studies.

Keywords:
alignment free methodsevolutionary distancephylogenetic reconstructionsequence similaritysuffix trees

More Related Videos

Construction of Synthetic Phage Displayed Fab Library with Tailored Diversity
12:31

Construction of Synthetic Phage Displayed Fab Library with Tailored Diversity

Published on: May 1, 2018

14.9K
Rare Event Detection Using Error-corrected DNA and RNA Sequencing
10:36

Rare Event Detection Using Error-corrected DNA and RNA Sequencing

Published on: August 3, 2018

12.7K

Related Experiment Videos

Last Updated: Mar 22, 2026

Proofreading and DNA Repair Assay Using Single Nucleotide Extension and MALDI-TOF Mass Spectrometry Analysis
11:08

Proofreading and DNA Repair Assay Using Single Nucleotide Extension and MALDI-TOF Mass Spectrometry Analysis

Published on: June 19, 2018

10.3K
Construction of Synthetic Phage Displayed Fab Library with Tailored Diversity
12:31

Construction of Synthetic Phage Displayed Fab Library with Tailored Diversity

Published on: May 1, 2018

14.9K
Rare Event Detection Using Error-corrected DNA and RNA Sequencing
10:36

Rare Event Detection Using Error-corrected DNA and RNA Sequencing

Published on: August 3, 2018

12.7K

Area of Science:

  • Bioinformatics
  • Computational Biology
  • Genomics

Background:

  • Alignment-free sequence comparison is crucial for large-scale genomic data analysis.
  • Existing methods struggle with computational complexity when accounting for sequence variations (mismatches).

Purpose of the Study:

  • To develop an efficient algorithm for the k-mismatch average common string (ACSk) problem.
  • To enable more accurate evolutionary modeling in sequence comparison.

Main Methods:

  • Developed a novel algorithm with O(n log(k) n) time and O(n) space complexity.
  • Extended the generalized suffix tree model to include perturbed suffixes.

Main Results:

  • Achieved the first provably efficient algorithm for the ACSk problem for any constant k.
  • Demonstrated potential for improved classification and approximate sequence matching.

Conclusions:

  • The new algorithm significantly advances sequence comparison capabilities by efficiently handling mismatches.
  • This method has broad applicability in molecular taxonomy, phylogenetics, and other bioinformatics tasks.