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Related Concept Videos

Conservation of Protein Domains Over Different Proteins02:26

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 form...
Conservation of Protein Domains02:26

Conservation of Protein Domains

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 form...
Phylogeny01:23

Phylogeny

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 kingdom.
Phylogenetic Trees03:21

Phylogenetic Trees

Phylogenetic trees come in many forms. It matters in which sequence the organisms are arranged from the bottom to the top of the tree, but the branches can rotate at their nodes without altering the information. The lines connecting individual nodes can be straight, angled, or even curved.
Phylogenetic Trees03:21

Phylogenetic Trees

Phylogenetic trees come in many forms. It matters in which sequence the organisms are arranged from the bottom to the top of the tree, but the branches can rotate at their nodes without altering the information. The lines connecting individual nodes can be straight, angled, or even curved.
Evolutionary Relationships through Genome Comparisons02:54

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...

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A Practical Guide to Phylogenetics for Nonexperts
12:00

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Cocos: Constructing multi-domain protein phylogenies.

Max Homilius1, John Wiedenhoeft, Sebastian Thieme

  • 1Dept. of Computer Science, Free University of Berlin, Germany; Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Berlin, Germany and Department of Vertebrate Genomics, Max Planck Institute for Molecular Genetics Berlin, Free University of Berlin, Germany.

Plos Currents
|June 21, 2011
PubMed
Summary
This summary is machine-generated.

Constructing phylogenies for multi-domain proteins is complex. Our new application infers ancestral proteins, handling incongruent domain phylogenies and identifying implausible evolutionary events.

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Last Updated: May 31, 2026

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Area of Science:

  • Evolutionary biology
  • Bioinformatics
  • Computational biology

Background:

  • Phylogenetic analysis of multi-domain proteins is challenging due to macro-evolutionary events.
  • Reconstructing protein evolutionary history requires integrating species and domain phylogenies.

Purpose of the Study:

  • To present a novel computational application for inferring ancestral multi-domain proteins.
  • To address the complexities arising from incongruent domain phylogenies.

Main Methods:

  • Implementation and extension of the algorithmic approach by Behzadi and Vingron (2006).
  • Development of diagnostics for identifying and reconciling implausible phylogenetic topologies.
  • Integration of species tree and domain phylogenies for ancestral reconstruction.

Main Results:

  • The application successfully infers ancestral multi-domain proteins.
  • Provided diagnostics aid in identifying and resolving topological conflicts in domain phylogenies.
  • The method extends previous algorithmic approaches for phylogenetic inference.

Conclusions:

  • The developed application simplifies the inference of ancestral multi-domain proteins.
  • The diagnostics are crucial for accurate phylogenetic reconstruction in the presence of conflicting data.
  • This work advances computational methods for studying protein evolution.