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Protein Families

Protein Families

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...

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...

Conservation of Protein Domains Over Different Proteins

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...

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Related Experiment Video

Updated: Apr 16, 2026

An Integrated Approach for Microprotein Identification and Sequence Analysis

An Integrated Approach for Microprotein Identification and Sequence Analysis

Published on: July 12, 2022

Fast and accurate multiple-protein-sequence alignment at scale with FAMSA2.

Adam Gudyś¹, Andrzej Zielezinski², Cedric Notredame^3,4,5

¹Faculty of Automatic Control, Electronics and Computer Science, Silesian University of Technology, Gliwice, Poland.

Nature Biotechnology

|April 14, 2026

Summary

This summary is machine-generated.

We developed FAMSA2, a fast and accurate algorithm for multiple protein sequence alignment. This new tool significantly speeds up the alignment of large protein families without sacrificing accuracy.

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Last Updated: Apr 16, 2026

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Area of Science:

Bioinformatics
Computational Biology
Genomics

Background:

Multiple protein sequence alignment is crucial for understanding protein function, evolution, and structure.
Existing alignment tools often struggle with scalability and speed when analyzing large protein families.

Purpose of the Study:

To introduce FAMSA2, a novel algorithm designed for high-accuracy and high-speed multiple protein sequence alignment.
To enable efficient analysis of massive protein families.

Main Methods:

FAMSA2 employs a progressive alignment strategy.
It utilizes medoid clustering for guide tree construction.
A dissimilarity measure based on the longest common subsequence is incorporated.

Main Results:

FAMSA2 achieves high accuracy comparable to state-of-the-art methods.
The algorithm runs approximately 400 times faster on average than existing aligners.
Performance was validated across structural, phylogenetic, and functional benchmarks.

Conclusions:

FAMSA2 offers a significant advancement in the speed and scalability of multiple protein sequence alignment.
It provides a powerful tool for researchers dealing with large-scale genomic and proteomic data analysis.