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The adaptive evolution database (TAED).

D A Liberles1, D R Schreiber, S Govindarajan

  • 1Departments of Chemistry, University of Florida, Gainesville, FL 32611, USA. liberles@sbc.su.se

Genome Biology
|September 5, 2001
PubMed
Summary
This summary is machine-generated.

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The Adaptive Evolution Database (TAED) identifies potential positive selection in protein families using evolutionary trees and KA/KS values. This resource aids researchers in finding adaptive evolution examples for further study.

Area of Science:

  • Evolutionary Biology
  • Genomics
  • Bioinformatics

Background:

  • The Master Catalog houses evolutionary data for GenBank genes, including alignments and phylogenetic trees.
  • This catalog supports large-scale genomic surveys, leading to the development of The Adaptive Evolution Database (TAED).

Purpose of the Study:

  • To identify and catalog instances of potential positive adaptation in protein families.
  • To provide a resource for researchers studying evolutionary processes and functional changes in proteins.

Main Methods:

  • Extracted evolutionary trees and ancestral sequences from the Master Catalog for Chordata and Embryophyta.
  • Identified branches with high normalized nonsynonymous to synonymous nucleotide substitution rates (KA/KS values) as indicators of positive selection.

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Main Results:

  • A significant proportion (10-20%) of examined protein families showed branches with high KA/KS values, suggesting positive selection.
  • Most identified candidate adaptive evolution episodes passed a robustness test and were included in TAED.

Conclusions:

  • TAED serves as a valuable resource for bioinformaticians and experimental evolutionists.
  • The database can be expanded to incorporate additional evolutionary data, such as gene regulation and splicing changes, within a phylogenetic context.