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Evolutionary rates at codon sites may be used to align sequences and infer protein domain function
Pierre M Durand1, Scott Hazelhurst, Theresa L Coetzer
1Evolutionary Medicine Unit, University of the Witwatersrand and National Health Laboratory Service, Johannesburg, South Africa. pierre.durand@wits.ac.za
BMC Bioinformatics
|March 26, 2010
Summary
A new algorithm, FIRE (Functional Inference using the Rates of Evolution), aligns sequences using evolutionary rates, enabling analysis of low-similarity sequences and protein domain function inference. This novel approach offers new possibilities in molecular biology research.
Area of Science:
- Molecular Biology
- Bioinformatics
- Evolutionary Biology
Background:
- Sequence alignment is crucial for molecular biology, but low sequence similarity poses significant challenges.
- Traditional methods struggle with fast-evolving genes, distant taxa, and convergent evolution.
Purpose of the Study:
- To develop a novel algorithm for aligning sequences with low similarity.
- To investigate the utility of evolutionary rates for sequence alignment and protein domain function inference.
Main Methods:
- Developed FIRE (Functional Inference using the Rates of Evolution) algorithm.
- Utilized codon site evolutionary rates (dN/dS ratio) for alignment.
- Tested FIRE on diverse datasets, including antibody variable regions.
Main Results:
- FIRE successfully aligned sequences with very low similarity.
- Alignments based on evolutionary rates can infer protein domain function.
- FIRE demonstrated potential for analyzing convergent evolution and low-similarity sequences.
Conclusions:
- FIRE proves that evolutionary rates can be used for sequence alignment and domain function inference.
- This represents a new paradigm in sequence analysis with broad molecular biology applications.
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