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 Repair01:20

Mismatch Repair

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...
Mismatch Repair01:36

Mismatch Repair

Overview
Fixing Double-strand Breaks02:04

Fixing Double-strand Breaks

The double-stranded structure of DNA has two major advantages. First, it serves as a safe repository of genetic information where one strand serves as the back-up in case the other strand is damaged. Second, the double-helical structure can be wrapped around proteins called histones to form nucleosomes, which can then be tightly wound to form chromosomes. This way, DNA chains up to 2 inches long can be contained within microscopic structures in a cell. A double-stranded break not only damages...
Fixing Double-strand Breaks02:04

Fixing Double-strand Breaks

The double-stranded structure of DNA has two major advantages. First, it serves as a safe repository of genetic information where one strand serves as the back-up in case the other strand is damaged. Second, the double-helical structure can be wrapped around proteins called histones to form nucleosomes, which can then be tightly wound to form chromosomes. This way, DNA chains up to 2 inches long can be contained within microscopic structures in a cell. A double-stranded break not only damages...

You might also read

Related Articles

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

Sort by
Same author

Mass spectrometry integrates protein design into structural biology method development.

QRB discovery·2026
Same author

Evaluating deep learning based structure prediction methods on antibody-antigen complexes.

Bioinformatics (Oxford, England)·2026
Same author

A deep learning framework for comprehensive prediction of human RNA G-quadruplex-binding proteins.

Bioinformatics (Oxford, England)·2026
Same author

Blind prediction of complex water and ion ensembles around RNA in CASP16.

bioRxiv : the preprint server for biology·2025
Same author

Blind Prediction of Complex Water and Ion Ensembles Around RNA in CASP16.

Proteins·2025
Same author

AlphaFold3 at CASP16.

Proteins·2025
Same journal

conMItion: an R package adjusting confounding factors for associations in multi-omics.

Bioinformatics (Oxford, England)·2026
Same journal

SpaMFG: a Spatial Multi-omics Integration Method based on Feature Grouping.

Bioinformatics (Oxford, England)·2026
Same journal

CSCN: Inference of Cell-Specific Causal Networks Using Single-Cell RNA-Seq Data.

Bioinformatics (Oxford, England)·2026
Same journal

Sparse CCA-Based Mediation Analysis with High-Dimensional Exposures and Mediators.

Bioinformatics (Oxford, England)·2026
Same journal

Enhancing Cross-Context Generalization in Drug Perturbation Prediction with a Multimodal Conditional Diffusion Framework.

Bioinformatics (Oxford, England)·2026
Same journal

Primer Design through Submodular Function Estimation.

Bioinformatics (Oxford, England)·2026
See all related articles

Related Experiment Video

Updated: Jun 2, 2026

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

KalignP: improved multiple sequence alignments using position specific gap penalties in Kalign2.

Nanjiang Shu1, Arne Elofsson

  • 1Department of Biochemistry and Biophysics, Stockholm Bioinformatics Center, Center for Biomembrane Research, Swedish e-science Research Center, Stockholm University, 106 91 Stockholm, Sweden.

Bioinformatics (Oxford, England)
|April 21, 2011
PubMed
Summary
This summary is machine-generated.

KalignP enhances multiple sequence alignment by incorporating position-specific gap penalties, improving accuracy over the original Kalign2 method. This new tool, KalignP, offers better performance on benchmark datasets.

More Related Videos

A Practical Guide to Phylogenetics for Nonexperts
12:00

A Practical Guide to Phylogenetics for Nonexperts

Published on: February 5, 2014

Creating and Applying a Reference to Facilitate the Discussion and Classification of Proteins in a Diverse Group
07:49

Creating and Applying a Reference to Facilitate the Discussion and Classification of Proteins in a Diverse Group

Published on: August 16, 2017

Related Experiment Videos

Last Updated: Jun 2, 2026

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

A Practical Guide to Phylogenetics for Nonexperts
12:00

A Practical Guide to Phylogenetics for Nonexperts

Published on: February 5, 2014

Creating and Applying a Reference to Facilitate the Discussion and Classification of Proteins in a Diverse Group
07:49

Creating and Applying a Reference to Facilitate the Discussion and Classification of Proteins in a Diverse Group

Published on: August 16, 2017

Area of Science:

  • Bioinformatics
  • Computational Biology
  • Genomics

Background:

  • Multiple sequence alignment (MSA) is fundamental in bioinformatics.
  • Existing methods like Kalign2 offer speed and accuracy but lack flexibility in gap penalty application.

Purpose of the Study:

  • To introduce KalignP, a modified version of Kalign2.
  • To enable KalignP to accept externally supplied position-specific gap penalties.

Main Methods:

  • KalignP was developed as a modification of the Kalign2 algorithm.
  • Position-specific gap penalties were derived from predicted secondary structures.
  • Performance was evaluated using Balibase 3.0 and Pfam-A seed alignments.

Main Results:

  • KalignP successfully integrates position-specific gap penalties.
  • The use of predicted secondary structure-derived penalties led to consistent improvements over Kalign2.
  • KalignP demonstrated enhanced accuracy in multiple sequence alignments.

Conclusions:

  • KalignP offers improved multiple sequence alignment accuracy compared to Kalign2.
  • The integration of position-specific gap penalties is a valuable enhancement for alignment methods.
  • KalignP provides a more flexible and accurate tool for bioinformatics research.