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Evolutionary distance estimation and fidelity of pair wise sequence alignment.
1Center for Evolutionary Functional Genomics, The Biodesign Institute, and The School of Life Sciences, Arizona State University, Tempe, AZ 84287-4501, USA. msr@asu.edu
BMC Bioinformatics
|April 21, 2005
Summary
Evolutionary distance estimation is robust to DNA sequence alignment errors when sequences are highly similar. However, significant alignment inaccuracies can skew results when sequence identity drops below 50%.
Area of Science:
- Genomics
- Molecular Evolutionary Biology
- Bioinformatics
Background:
- Evolutionary distances are fundamental in comparative genomics and molecular evolution.
- Assessing alignment accuracy's impact on evolutionary distance is crucial.
Purpose of the Study:
- To investigate how DNA sequence alignment accuracy affects evolutionary distance estimation.
- To determine the threshold of alignment error impacting distance calculations.
Main Methods:
- A simulation study was conducted.
- Examined the effect of alignment error on evolutionary distance estimation under various conditions.
Main Results:
- Distance estimation remained largely unaffected by alignment errors (≥50% incorrect sites) if sequence identity was high (≥50%).
- Beyond this threshold, alignment errors artificially inflated sequence identity, distorting distance estimates.
- Results were independent of substitution models, sequence length, and indel parameters.
Conclusions:
- Estimated sequence identity can indicate alignment accuracy.
- Analyses relying on evolutionary distance may tolerate some alignment error if divergence is limited (<50%).
- Site-specific analyses are more sensitive to alignment inaccuracies than distance-based analyses.