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Asymmetric exclusion process and extremal statistics of random sequences
1Department of Physics, University of California at San Diego, La Jolla, California 92093-0319, USA.
Summary
This study links computational biology sequence alignment to nonequilibrium physics models. Analyzing the hopping current in the asymmetric exclusion process helps determine the statistical significance of sequence alignments.
Area of Science:
- Computational Biology
- Nonequilibrium Physics
- Statistical Mechanics
Background:
- Sequence alignment is a fundamental tool in computational biology for comparing biological sequences.
- The asymmetric exclusion process is an exactly solvable model in nonequilibrium statistical mechanics.
Purpose of the Study:
- To establish a novel mapping between sequence alignment parameters and the asymmetric exclusion process.
- To utilize concepts from statistical physics to characterize the statistical significance of sequence alignments.
Main Methods:
- Developing a theoretical framework to connect sequence alignment scoring parameters with the asymmetric exclusion process.
- Analyzing the total hopping current in a discrete time and space version of the asymmetric exclusion process.
Main Results:
- A direct correspondence was found between specific sequence alignment scoring choices and the asymmetric exclusion process.
- The statistical significance of sequence alignments can be quantified by studying the hopping current.
Conclusions:
- This interdisciplinary approach offers new insights into understanding sequence alignment significance.
- The findings bridge computational biology and physics, providing a novel analytical tool.