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TreeDom: a graphical web tool for analysing domain architecture evolution.

Christian Haider1, Marina Kavic1, Erik L L Sonnhammer2

  • 1Stockholm Bioinformatics Center, Department of Biochemistry and Biophysics, Stockholm University, Science for Life Laboratory, Solna SE-17121, Sweden FH OÖ - University of Applied Sciences Upper Austria, Hagenberg 4232, Austria.

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Summary

TreeDom is a web tool that visualizes the evolutionary history of protein domains. It helps researchers understand protein function by analyzing domain duplication, origin, and loss patterns within protein families.

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Area of Science:

  • Evolutionary biology
  • Bioinformatics
  • Structural biology

Background:

  • Understanding the evolutionary history of protein domains is crucial for deciphering protein function and evolution.
  • Individual domains within a multi-domain protein can exhibit distinct evolutionary trajectories, impacting overall protein behavior.
  • Previous methods lacked integrated visualization for domain evolution analysis within protein families.

Purpose of the Study:

  • To introduce TreeDom, a novel web tool for graphical analysis of evolutionary histories of domains in multi-domain proteins.
  • To provide insights into domain duplication, insertion, and loss events within protein families.
  • To facilitate the understanding of how domain evolution shapes protein function.

Main Methods:

  • TreeDom utilizes the Pfam database for domain annotations.
  • It constructs and displays phylogenetic trees based on sequence alignments of selected protein sequences.
  • Domain architectures are visualized alongside the sequence tree for each protein.

Main Results:

  • TreeDom graphically represents the evolutionary relationships of domains across protein sequences.
  • The tool allows users to focus analysis on a specified number of most similar sequences or a custom list of IDs.
  • It integrates domain architecture information with phylogenetic data.

Conclusions:

  • TreeDom offers a user-friendly platform for exploring complex domain evolution patterns.
  • The tool aids in understanding the evolutionary origins and functional implications of domain arrangements in proteins.
  • It serves as a valuable resource for researchers in evolutionary biology and protein science.