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Where does the alignment score distribution shape come from?

Philippe Ortet¹, Olivier Bastien

¹CNRS (UMR 6191)-CEA Cadarache-Aix-Marseille Université, Laboratoire d'Ecologie Microbienne de la Rhizosphere, Institut de Biologie Environementale et Biotechnologie, CEA Cadarache, F-13108 Saint Paul-lez-Durance, France.

Evolutionary Bioinformatics Online

|January 25, 2011

Summary

This summary is machine-generated.

This study explores the evolutionary origins of protein sequence alignment score distributions. We propose a novel model based on protein evolution, offering a better-performing alternative to existing methods.

Keywords:

Karlin-Altchul theorem mutual information sequence alignment scores sequence space

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Area of Science:

Bioinformatics
Computational Biology
Evolutionary Biology

Background:

Protein sequence alignment algorithms are crucial for identifying homologous proteins and generate score distributions resembling extreme value distributions.
The evolutionary origin of these score distributions has remained an open question for two decades.

Purpose of the Study:

To investigate the evolutionary basis of protein sequence alignment score distributions.
To derive the properties of these distributions from a fundamental protein evolution process.

Main Methods:

Modeling protein evolution as a duplication-divergence process within a sequence space.
Defining sequence distribution based on genetic distance.
Establishing a relationship between genetic distance and alignment scores.

Main Results:

A novel score probability distribution was derived.
The derived distribution is qualitatively similar to the Karlin-Altschul distribution.
The new model demonstrates superior performance compared to previous models.

Conclusions:

The duplication-divergence model provides a plausible evolutionary explanation for sequence alignment score distributions.
This research offers a more accurate predictive model for sequence alignment analysis.