Understanding Variation in Protein Sequence Identity Calculations
Author Information
Author(s): Raghava GP, Barton Geoffrey J
Primary Institution: University of Dundee
Hypothesis
How does the method of calculating percentage identity (PID) affect the reported values in protein sequence alignments?
Conclusion
The study shows that different methods of calculating percentage identity can lead to significant variations, highlighting the need for careful interpretation of PID values.
Supporting Evidence
- The maximum variation in PID due to the calculation method was 11.5%.
- The effect of alignment algorithm on PID was up to 14.6%.
- The combined effect of alignment algorithm and PID calculation gave a variation of up to 22%.
- PID calculations that consider gaps were more correlated with structural similarity than those that do not.
Takeaway
This study found that the way we calculate how similar two proteins are can change a lot depending on the method used, so we need to be careful when using these numbers.
Methodology
The study systematically quantified the variation in PID across 1028 protein sequence alignments using different calculation methods and alignment algorithms.
Limitations
The study does not address the application of PID in estimating phylogenetic trees or the effects of other alignment parameters.
Digital Object Identifier (DOI)
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