Where Does the Alignment Score Distribution Shape Come from?

Where Does the Alignment Score Distribution Shape Come from?

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Alignment algorithms are powerful tools for searching for homologous proteins in databases, providing a score for each sequence present in the database. It has been well known for 20 years that the shape of the score distribution looks like an extreme value distribution. The extremely large number o...

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Main Authors: Philippe Ortet, Olivier Bastien
Format: Article
Language:English
Published: SAGE Publishing 2010-01-01
Series:Evolutionary Bioinformatics
Online Access:https://doi.org/10.4137/EBO.S5875
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spelling doaj-901a6e9be9db4520bf379a6833c0cef32020-11-25T03:40:40ZengSAGE PublishingEvolutionary Bioinformatics1176-93432010-01-01610.4137/EBO.S5875Where Does the Alignment Score Distribution Shape Come from?Philippe Ortet0Olivier Bastien1CNRS (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.UMR 5168 CNRS-CEA-INRA Université J. Fourier, Laboratoire de Physiologie Cellulaire Végétale, Département Réponse et Dynamique Cellulaire, CEA Grenoble, 17 rue des Martyrs, F-38054, Grenoble cedex 09, France.Alignment algorithms are powerful tools for searching for homologous proteins in databases, providing a score for each sequence present in the database. It has been well known for 20 years that the shape of the score distribution looks like an extreme value distribution. The extremely large number of times biologists face this class of distributions raises the question of the evolutionary origin of this probability law. We investigated the possibility of deriving the main properties of sequence alignment score distributions from a basic evolutionary process: a duplication-divergence protein evolution process in a sequence space. Firstly, the distribution of sequences in this space was defined with respect to the genetic distance between sequences. Secondly, we derived a basic relation between the genetic distance and the alignment score. We obtained a novel score probability distribution which is qualitatively very similar to that of Karlin-Altschul but performing better than all other previous model.https://doi.org/10.4137/EBO.S5875
collection DOAJ
language English
format Article
sources DOAJ
author Philippe Ortet
Olivier Bastien
spellingShingle Philippe Ortet
Olivier Bastien
Where Does the Alignment Score Distribution Shape Come from?
Evolutionary Bioinformatics
author_facet Philippe Ortet
Olivier Bastien
author_sort Philippe Ortet
title Where Does the Alignment Score Distribution Shape Come from?
title_short Where Does the Alignment Score Distribution Shape Come from?
title_full Where Does the Alignment Score Distribution Shape Come from?
title_fullStr Where Does the Alignment Score Distribution Shape Come from?
title_full_unstemmed Where Does the Alignment Score Distribution Shape Come from?
title_sort where does the alignment score distribution shape come from?
publisher SAGE Publishing
series Evolutionary Bioinformatics
issn 1176-9343
publishDate 2010-01-01
description Alignment algorithms are powerful tools for searching for homologous proteins in databases, providing a score for each sequence present in the database. It has been well known for 20 years that the shape of the score distribution looks like an extreme value distribution. The extremely large number of times biologists face this class of distributions raises the question of the evolutionary origin of this probability law. We investigated the possibility of deriving the main properties of sequence alignment score distributions from a basic evolutionary process: a duplication-divergence protein evolution process in a sequence space. Firstly, the distribution of sequences in this space was defined with respect to the genetic distance between sequences. Secondly, we derived a basic relation between the genetic distance and the alignment score. We obtained a novel score probability distribution which is qualitatively very similar to that of Karlin-Altschul but performing better than all other previous model.
url https://doi.org/10.4137/EBO.S5875
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AT olivierbastien wheredoesthealignmentscoredistributionshapecomefrom
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