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

Evolutionary Relationships through Genome Comparisons02:54

Evolutionary Relationships through Genome Comparisons

6.8K
Genome comparison is one of the excellent ways to interpret the evolutionary relationships between organisms. The basic principle of genome comparison is that if two species share a common feature, it is likely encoded by the DNA sequence conserved between both species. The advent of genome sequencing technologies in the late 20th century enabled scientists to understand the concept of conservation of domains between species and helped them to deduce evolutionary relationships across diverse...
6.8K
Protein Families02:47

Protein Families

16.5K
Protein families are groups of homologous proteins; that is, they have similarities in amino acid sequences and three-dimensional structures. Protein families usually occur because of gene duplication, where an additional copy of a gene is inserted into the genome of an organism.   Mutations that change the amino acids but still allow the protein to be properly synthesized, will lead to new protein family members.   If these new proteins contain similar amino acids in key...
16.5K
Conserved Binding Sites01:49

Conserved Binding Sites

5.0K
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...
5.0K
Protein-protein Interfaces02:04

Protein-protein Interfaces

14.4K
Many proteins form complexes to carry out their functions, making protein-protein interactions (PPIs) essential for an organism's survival. Most PPIs are stabilized by numerous weak noncovalent chemical forces. The physical shape of the interfaces determines the way two proteins interact. Many globular proteins have closely-matching shapes on their surfaces, which form a large number of weak bonds. Additionally, many PPIs occur between two helices or between a surface cleft and a...
14.4K
Protein Networks02:26

Protein Networks

4.4K
An organism can have thousands of different proteins, and these proteins must cooperate to ensure the health of an organism. Proteins bind to other proteins and form complexes to carry out their functions. Many proteins interact with multiple other proteins creating a complex network of protein interactions.
These interactions can be represented through maps depicting protein-protein interaction networks, represented as nodes and edges. Nodes are circles that are representative of a protein,...
4.4K
Conservation of Protein Domains Over Different Proteins02:26

Conservation of Protein Domains Over Different Proteins

13.9K
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...
13.9K

You might also read

Related Articles

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

Sort by
Same author

MUFOLD-DB: a processed protein structure database for protein structure prediction and analysis.

BMC genomics·2015
Same author

Advances in translational bioinformatics facilitate revealing the landscape of complex disease mechanisms.

BMC bioinformatics·2015
Same author

The I-TASSER Suite: protein structure and function prediction.

Nature methods·2014
Same author

Genome-wide expression analysis of soybean NF-Y genes reveals potential function in development and drought response.

Molecular genetics and genomics : MGG·2014
Same author

Classification of lung cancer using ensemble-based feature selection and machine learning methods.

Molecular bioSystems·2014
Same author

Resveratrol possesses protective effects in a pristane-induced lupus mouse model.

PloS one·2014
Same journal

De Novo Protein Design Using the Blueprint Builder in Rosetta.

Current protocols in protein science·2020
Same journal

Methods for Expression of Recombinant Proteins Using a Pichia pastoris Cell-Free System.

Current protocols in protein science·2020
Same journal

Histone Purification Combined with High-Resolution Mass Spectrometry to Examine Histone Post-Translational Modifications and Histone Variants in Caenorhabditis elegans.

Current protocols in protein science·2020
Same journal

A Rapid and Facile Purification Method for Glycan-Binding Proteins and Glycoproteins.

Current protocols in protein science·2020
Same journal

Synthesis of Recombinant Human Hemoglobin With NH<sub>2</sub> -Terminal Acetylation in Escherichia coli.

Current protocols in protein science·2020
Same journal

A Fluorescence-Based Assay to Monitor SUMOylation in Real-Time.

Current protocols in protein science·2020
See all related articles

Related Experiment Video

Updated: Dec 30, 2025

Application of I TASSER, trRosetta, UCSF Chimera, HADDOCK server, and HEX loria for De Novo and In Silico Design of Proteins
05:08

Application of I TASSER, trRosetta, UCSF Chimera, HADDOCK server, and HEX loria for De Novo and In Silico Design of Proteins

Published on: July 8, 2025

840

Computational methods for protein sequence comparison and search.

Dong Xu1

  • 1Department of Computer Science and Christopher S. Bond Life Sciences Center, University of Missouri-Columbia, Columbia, Missouri.

Current Protocols in Protein Science
|April 15, 2009
PubMed
Summary
This summary is machine-generated.

This guide explains protein sequence analysis tools for researchers. It covers essential methods like sequence comparison, database searching, and alignment for understanding gene function and evolution.

More Related Videos

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

7.4K
A Protocol for Computer-Based Protein Structure and Function Prediction
16:41

A Protocol for Computer-Based Protein Structure and Function Prediction

Published on: November 3, 2011

69.6K

Related Experiment Videos

Last Updated: Dec 30, 2025

Application of I TASSER, trRosetta, UCSF Chimera, HADDOCK server, and HEX loria for De Novo and In Silico Design of Proteins
05:08

Application of I TASSER, trRosetta, UCSF Chimera, HADDOCK server, and HEX loria for De Novo and In Silico Design of Proteins

Published on: July 8, 2025

840
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

7.4K
A Protocol for Computer-Based Protein Structure and Function Prediction
16:41

A Protocol for Computer-Based Protein Structure and Function Prediction

Published on: November 3, 2011

69.6K

Area of Science:

  • Bioinformatics
  • Computational Biology
  • Genomics

Background:

  • Protein sequence analysis is crucial for understanding gene function, structure, and evolution.
  • Exponential growth in sequence data necessitates efficient analysis tools.
  • Accessible web-based tools are vital for both bioinformatics researchers and experimental biologists.

Purpose of the Study:

  • To provide theoretical background on protein sequence comparison and search.
  • To describe popular bioinformatics tools for sequence analysis.
  • To offer practical guidance on using these tools for biological inference.

Main Methods:

  • Dot plot analysis for visual sequence comparison.
  • Database searching for identifying homologous sequences.
  • Multiple sequence alignments for evolutionary and functional insights.
  • Phylogenetic tree construction for evolutionary relationships.
  • Protein family and motif searching for functional domain identification.

Main Results:

  • Demonstration of popular web-based tools for various sequence analysis tasks.
  • Step-by-step examples for practical application of selected tools.
  • Guidance on integrating different analysis tools for robust biological conclusions.

Conclusions:

  • Effective use of sequence analysis tools aids in inferring protein function, structure, and evolutionary history.
  • Accessible bioinformatics tools empower biologists with limited computational expertise.
  • Combining diverse sequence analysis methods enhances biological discovery and inference.