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Updated: Sep 22, 2025

Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues
Published on: July 14, 2015
OrthoQuantum: visualizing evolutionary repertoire of eukaryotic proteins
Ivan S Ilnitskiy1,2, Anastasia A Zharikova1,2, Andrey A Mironov1,2
1Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Lomonosovsky Prospect 27, Building 10, 119991 Moscow, Russia.
Orthology analysis is streamlined with OrthoQuantum, a web server for visualizing eukaryotic protein phylogenetic profiles. This tool aids in identifying co-evolutionary patterns and lineage-specific innovations from large omics datasets.
Area of Science:
- Bioinformatics
- Computational Biology
- Evolutionary Genomics
Background:
- Next-generation sequencing and omics studies generate vast evolutionary data.
- Understanding protein evolution requires efficient analysis of orthologous sequences.
- Existing tools may lack comprehensive visualization of phylogenetic profiles.
Purpose of the Study:
- To present OrthoQuantum, a web server for analyzing eukaryotic protein phylogenetic profiles.
- To enable time-efficient visualization of evolutionary patterns.
- To facilitate the identification of coupled evolutionary trends and lineage-specific innovations.
Main Methods:
- Utilizes open-source databases of orthologous sequences across diverse taxa.
- Employs binary vectors to represent protein conservation patterns (presence/absence).
- Calculates correlation pairs to identify co-inherited proteins and visualizes profiles with phylogenetic trees.
Main Results:
- OrthopQuantum provides a user-friendly interface for querying gene names and UniProt identifiers.
- The server supports analysis across different phylogenetic clades with optional BLAST searches.
- Visualizations integrate phylogenetic trees with protein conservation profiles.
Conclusions:
- OrthopQuantum offers an efficient solution for exploring the evolutionary landscape of eukaryotic proteins.
- The tool aids researchers in defining lineage-specific innovations through coupled evolutionary analysis.
- Freely available web server facilitates broad accessibility for the scientific community.
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