Related Experiment Video
Updated: Jun 10, 2026
10:23
A Concoction Pipeline for Generating Molecular Operational Taxonomic Units (MOTUs) Among Riparian and Aquatic Beetles
Published on: July 11, 2025
Structome-TM: complementing dataset assembly for structural phylogenetics by addressing size-based biases
Ashar J Malik1,2,3, David B Ascher1,2,3
1School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, 4072, Australia.
Bioinformatics Advances
|June 9, 2026
Summary
Structome-TM aids in uncovering evolutionary relationships by identifying homologous proteins missed by global alignment. This web resource uses local structural similarity to build comprehensive protein structural neighborhoods for phylogenetic analysis.
Area of Science:
- Structural bioinformatics
- Computational biology
- Evolutionary biology
Background:
- Effective comparison of protein structures is crucial for understanding evolutionary relationships.
- Global alignment methods struggle with homologous proteins of varying sizes or domain architectures.
Purpose of the Study:
- Introduce Structome-TM, a web resource for assembling datasets for phylogenetic reconstruction.
- Address limitations of global alignment in identifying distant evolutionary relationships.
Main Methods:
- Utilizes Template Modelling score for prioritizing local structural similarity.
- Accepts Protein Data Bank identifiers, user-uploaded structures, and protein sequences as input.
- Predicts protein structures in real-time for sequence-based queries.
Main Results:
- Excels at identifying obscured homologous relationships based on local structural similarity.
- Enables the construction of comprehensive protein structural neighborhoods.
- Facilitates phylogenetic analysis even when experimentally determined structures are unavailable.
Conclusions:
- Structome-TM offers a powerful approach for exploring protein evolution.
- The resource enhances the discovery of deep evolutionary connections through structural comparisons.
- Provides a user-friendly interface for assembling phylogenetic datasets.
Related Concept Videos
03:36Genome Annotation and Assembly
The genome refers to all of the genetic material in an organism. It can range from a few million base pairs in microbial cells to several billion base pairs in many eukaryotic organisms. Genome assembly refers to the process of taking the DNA sequencing data and putting it all back together in a correct order to create a close representation of the original genome. This is followed by the identification of functional elements on the newly assembled genome, a process called genome annotation.
02:54Evolutionary 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...
01:23Phylogeny
Phylogeny is concerned with the evolutionary diversification of organisms or groups of organisms. A group of organisms with a name is called a taxon (singular). Taxa (plural) can span different levels of the evolutionary hierarchy. For instance, the group containing all birds is a taxon (comprising the class Aves), and the group of all species of daisies (the genus Bellis) is a taxon. Phylogenies can likewise include just one genus (i.e., depict species relationships) or span an entire...
02:51Multi-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...
Although the genome of each species varies greatly from each other, a few sequences are highly conserved. Such conserved DNA...
01:28Microbial 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,...
01:29Modern 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...