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

Conservation of Protein Domains Over Different Proteins02:26

Conservation of Protein Domains Over Different Proteins

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 form...
Conservation of Protein Domains02:26

Conservation of Protein Domains

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 form...
Conserved Binding Sites01:49

Conserved Binding Sites

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 analyses the...
Conserved Binding Sites01:49

Conserved Binding Sites

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 analyses the...
Globular Proteins01:27

Globular Proteins

In organisms, proteins are the most abundant macromolecules. They act as the building blocks of life and play various crucial roles in the body. Proteins can be broadly classified into two distinct subtypes based on their shape and solubilities: globular proteins and fibrous proteins.
Globular proteins serve many important physiological functions, such as acting as enzymes, cellular messengers, and molecular transporters. These roles often require the proteins to be soluble in the aqueous...
Globular and Fibrous Proteins02:21

Globular and Fibrous Proteins

Many proteins can be classified into two distinct subtypes - globular or fibrous. These two types differ in their shapes and solubilities.
Globular proteins are also known as spheroproteins and typically are approximately round in shape. They contain a mix of amino acid types and contain differing sequences in their primary structures. Globular proteins have many different functions, such as enzymes, cellular messengers, and molecular transporters. These roles often require the proteins to be...

You might also read

Related Articles

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

Sort by
Same author

Control of retrotransposon-driven activation of the interferon response by the double-stranded RNA binding protein DGCR8.

Nucleic acids research·2026
Same author

Calcium Reduces Fruit Abscission in <i>Persimmon</i> by Targeting Cell Wall Integrity.

Plants (Basel, Switzerland)·2025
Same author

BMAL1-TRIM28 represses transposable elements independently of CLOCK in pluripotent cells.

Nature communications·2025
Same author

DGCR8 haploinsufficiency leads to primate-specific RNA dysregulation and pluripotency defects.

Nucleic acids research·2025
Same author

Reversion of fruit-dependent inhibition of flowering in Citrus requires sprouting of buds with epigenetically silenced CcMADS19.

The New phytologist·2021
Same author

The tumor suppressor microRNA let-7 inhibits human LINE-1 retrotransposition.

Nature communications·2020

Related Experiment Video

Updated: May 29, 2026

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

Normalized global alignment for protein sequences.

Guillermo Peris1, Andrés Marzal

  • 1Department de Llenguatges i Sistemes Informátics, Universitat Jaume I, 12071 Castelló, Spain. peris@lsi.uji.es

Journal of Theoretical Biology
|September 28, 2011
PubMed
Summary

A new normalized global alignment score corrects length dependence in protein comparisons. This method offers a computationally cheaper and effective alternative to Z-scores for identifying homologous proteins.

More Related Videos

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

An Integrated Approach for Microprotein Identification and Sequence Analysis
09:37

An Integrated Approach for Microprotein Identification and Sequence Analysis

Published on: July 12, 2022

Related Experiment Videos

Last Updated: May 29, 2026

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

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

An Integrated Approach for Microprotein Identification and Sequence Analysis
09:37

An Integrated Approach for Microprotein Identification and Sequence Analysis

Published on: July 12, 2022

Area of Science:

  • Bioinformatics
  • Computational Biology
  • Structural Biology

Background:

  • Global alignment is crucial for comparing protein sequences, particularly in phylogenetic research.
  • Traditional global alignment scores can be influenced by sequence length and composition.
  • Z-score computation using Monte Carlo methods is effective but computationally expensive due to extensive sequence alignments.

Purpose of the Study:

  • To introduce a normalized global alignment score to mitigate length dependence in protein comparisons.
  • To develop an efficient algorithm for computing this normalized score.
  • To evaluate the normalized score's effectiveness in homologous protein detection and its relationship with Z-score.

Main Methods:

  • A novel normalized global alignment score was defined as the optimal ratio of alignment score to sequence length.
  • An algorithm based on fractional programming was implemented for efficient computation.
  • Experiments were conducted using proteins from the SCOP ASTRAL database to assess performance.

Main Results:

  • The normalized global alignment score demonstrates a linear relationship with the Z-score.
  • Its computational cost is significantly lower, equivalent to approximately 2.5 Needleman-Wunsch runs.
  • The normalized score enhances the detection of homologous proteins compared to traditional methods.

Conclusions:

  • Normalized global alignment serves as a cost-effective substitute for computationally intensive Z-scores.
  • This approach improves the accuracy and efficiency of identifying homologous proteins.
  • The developed software is publicly available for broader research application.