Search research articles

ABOUT JoVE

Overview Leadership Blog JoVE Help Center

AUTHORS

Publishing Process Editorial Board Scope & Policies Peer Review FAQ Submit

LIBRARIANS

Testimonials Subscriptions Access Resources Library Advisory Board FAQ

RESEARCH

JoVE Journal Methods Collections JoVE Encyclopedia of Experiments Archive

EDUCATION

JoVE Core JoVE Business JoVE Science Education JoVE Lab Manual Faculty Resource Center Faculty Site

Terms & Conditions of Use

Related Concept Videos

Evolutionary Relationships through Genome Comparisons

Evolutionary Relationships through Genome Comparisons

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...

Modern Molecular Taxonomy

Modern Molecular Taxonomy

Advancements in molecular biology have revolutionized the identification and characterization of bacteria, with multiple methods leveraging DNA sequencing for enhanced precision. As sequencing technologies improve and costs decline, these approaches are increasingly used in clinical, environmental, and evolutionary studies.Multilocus Sequence Typing (MLST) examines several housekeeping genes, essential chromosomal genes encoding cellular functions, to distinguish strains. Approximately...

Microbial Phylogeny

Microbial Phylogeny

Understanding the evolutionary relationships among microorganisms is fundamental to microbial ecology and taxonomy. Phylogenetic trees are essential tools for inferring these relationships, relying primarily on comparative analyses of molecular sequences such as DNA, RNA, or proteins. In microbial studies, these trees typically depict the evolutionary paths of diverse bacterial and archaeal species by mapping genetic differences accumulated over time.Phylogenetic trees are composed of tips,...

Gene Evolution - Fast or Slow?

Gene Evolution - Fast or Slow?

The genomes of eukaryotes are punctuated by long stretches of sequence which do not code for proteins or RNAs. Although some of these regions do contain crucial regulatory sequences, the vast majority of this DNA serves no known function. Typically, these regions of the genome are the ones in which the fastest change, in evolutionary terms, is observed, because there is typically little to no selection pressure acting on these regions to preserve their sequences.
In contrast, regions which code...

Multi-species Conserved Sequences

Multi-species Conserved Sequences

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 DNA...

Conserved Binding Sites

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...

You might also read

Related Articles

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

Sort by

Same author

Comparative transcriptomic insights into iron deficiency response in contrasting rice varieties at the seedling stage reveal distinct response strategies and identify novel candidate genes.

Frontiers in plant science·2026

Same author

Emerging strategies for computational identification of protein-protein interaction hotspots.

Current opinion in structural biology·2026

Same author

GRAYU: graph-based database integrating Ayurvedic formulations, medicinal plants, phytochemicals and diseases.

Frontiers in pharmacology·2026

Same author

Computational Analyses of Bifurcated Inter-Protein Interactions in Protein-Protein Assemblies Reveal Their Pivotal Role in Conferring Stability.

Proteins·2025

Same author

SIRT2 attenuates stress-induced skeletal muscle atrophy by inhibiting glucocorticoid receptor signalling.

bioRxiv : the preprint server for biology·2025

Same author

PASS2: update of database of structure-based sequence alignments.

Database : the journal of biological databases and curation·2025

Search research articles

Related Experiment Video

Updated: Jun 3, 2026

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

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

Published on: August 16, 2017

Critical assessment of structure-based sequence alignment methods at distant relationships.

Singarevelu Kalaimathy¹, Ramanathan Sowdhamini, Karuppiah Kanagarajadurai

¹National Centre for Biological Sciences (TIFR), GKVK Campus, Bellary Road, Bangalore 560065, India.

Briefings in Bioinformatics

|March 23, 2011

Summary

Accurate protein sequence alignment is challenging for distant relationships. Methods comparing fragments with twists and translations show better results for proteins with low sequence identity and varying lengths.

More Related Videos

Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin

Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin

Published on: August 14, 2018

A Protocol for Computer-Based Protein Structure and Function Prediction

A Protocol for Computer-Based Protein Structure and Function Prediction

Published on: November 3, 2011

Related Experiment Videos

Last Updated: Jun 3, 2026

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

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

Published on: August 16, 2017

Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin

Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin

Published on: August 14, 2018

A Protocol for Computer-Based Protein Structure and Function Prediction

A Protocol for Computer-Based Protein Structure and Function Prediction

Published on: November 3, 2011

Area of Science:

Computational biology
Structural bioinformatics
Protein structure analysis

Background:

Accurate protein sequence alignment is essential for protein modeling and evolutionary studies.
Achieving reliable alignments becomes difficult when protein sequences share low similarity (distant relationships).

Purpose of the Study:

To evaluate the performance of different sequence alignment programs for proteins with distant evolutionary relationships.
To identify alignment methods that are robust to variations in domain size and length.

Main Methods:

Performed 3,052 sequence alignments on 218 protein domain pairs with <40% sequence identity.
Included domains from diverse structural classes, sizes, and with rigid/variable lengths.
Assessed alignments using structural parameters like root mean square deviation and secondary-structural content.

Main Results:

Alignment methods that utilize fragment comparison and allow for structural variations (twists, translations) performed best.
These fragment-based methods demonstrated superior performance in distant relationship scenarios and with length variations.

Conclusions:

Fragment-based alignment strategies are effective for challenging protein sequence alignments.
These methods improve the accuracy of evolutionary modeling for distantly related proteins.