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Updated: Jul 20, 2026
07:49
Creating and Applying a Reference to Facilitate the Discussion and Classification of Proteins in a Diverse Group
Published on: August 16, 2017
Data mining for proteins characteristic of clades
Marshall Bern1, David Goldberg, Eugenia Lyashenko
1Palo Alto Research Center, 3333 Coyote Hill Road, Palo Alto, CA 94304, USA. bern@parc.com
Nucleic Acids Research
|August 29, 2006
Summary
A new program, Conserv, efficiently identifies molecular synapomorphies across genomes. This tool aids in discovering evolutionary relationships and classifying bacterial clades using genetic data.
Area of Science:
- Evolutionary Biology
- Genomics
- Bioinformatics
Background:
- Synapomorphies are crucial for inferring evolutionary relationships.
- Identifying molecular synapomorphies across genomes is challenging due to data volume.
- Existing tools lack efficient genome-wide search capabilities for synapomorphies.
Purpose of the Study:
- To develop a computational tool for rapid identification of molecular synapomorphies.
- To enable large-scale searches for synapomorphies within bacterial clades.
- To facilitate the study of evolutionary history using genomic data.
Main Methods:
- Development of the Conserv program for assembling orthologous sequences.
- Ranking of sequences by conservation and divergence metrics.
- Application of Conserv for genome-wide synapomorphy searches in bacteria.
Main Results:
- Conserv rapidly identifies and ranks orthologous sequences.
- Discovery of clade-specific sequences for Actinobacteria, Firmicutes, and gamma-Proteobacteria.
- Provided evidence for the phylogenetic placement of Symbiobacterium thermophilum.
Conclusions:
- Conserv is an effective tool for large-scale molecular synapomorphy searches.
- The program aids in resolving evolutionary questions in bacterial phylogeny.
- Facilitates the use of genomic data for evolutionary inference.
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