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Creating and Applying a Reference to Facilitate the Discussion and Classification of Proteins in a Diverse Group
Published on: August 16, 2017
Tracing globin phylogeny using PSIBLAST searches based on groups of sequences
1Department of Biochemistry and Molecular Biology, School of Medicine, Wayne State University, Detroit, Michigan, USA.
Methods in Enzymology
|February 2, 2008
Summary
Protein sequence similarity searches using PSIBLAST reveal evolutionary relationships between globin families. The distribution breadth of search scores may indicate a globin group's evolutionary age.
Area of Science:
- Bioinformatics
- Computational Biology
- Evolutionary Biology
Background:
- Protein sequence similarity searches are crucial for identifying evolutionary relationships.
- Iterative PSIBLAST searches detect distant homologs and can reveal broader evolutionary connections.
Purpose of the Study:
- To investigate the utility of PSIBLAST score distributions for inferring globin evolutionary relationships.
- To explore the correlation between score distribution breadth and the evolutionary age of globin families.
Main Methods:
- Performed PSIBLAST searches using various vertebrate globin sequences as queries.
- Analyzed histograms of E values and bit scores to assess sequence similarity distributions.
- Compared PSIBLAST results with established globin phylogenetic trees.
Main Results:
- PSIBLAST score distributions were congruent with the accepted globin phylogenetic tree.
- Neuroglobins showed similarity to bacterial globins, highlighting distant evolutionary links.
- Ancient globin lineages exhibited broad score distributions, while recent groups like cytoglobins showed narrow distributions.
Conclusions:
- PSIBLAST score distributions provide insights into globin evolutionary history and relationships.
- The breadth of score distributions may serve as a proxy for the evolutionary age of globin families.
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