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Bioinformatics Advance Access published online on January 22, 2007
Bioinformatics, doi:10.1093/bioinformatics/btm005
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© The Author (2007). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

SatDNA Analyzer: a computing tool for satellite-DNA evolutionary analysis

Rafael Navajas-Pérez 1,{dagger},*, Cristina Rubio-Escudero 2,{dagger}, José Luis Aznarte 2,{dagger}, Manuel Ruiz Rejón 1 and Manuel A. Garrido-Ramos 1

1Departamento de Genética, Facultad de Ciencias, Universidad de Granada, 18071, Granada, SPAIN 2Departamento de Ciencias de la Computación e Inteligencia Artificial, Universidad de Granada, Granada, SPAIN
{dagger}These authors have contributed equally to this work.

*To whom correspondence should be addressed. Rafael Navajas-Pérez, E-mail: rnavajas{at}uga.edu


  Abstract

SUMMARY

satDNA Analyzer is a program, implemented in C++, for the analysis of the patterns of variation at each nucleotide position considered independently amongst all units of a given satellite-DNA family when comparing it between a pair of species. The program classifies each site accordingly as monomorphic or polymorphic, discriminates shared from non-shared polymorphisms and classifies each non-shared polymorphism according to the model proposed by Strachan et al. (1985) in six different stages of transition during the spread of a variant repeat unit toward its fixation. Furthermore, this program implements several other utilities for satellite-DNA analysis evolution such as the design of the average consensus sequences, the average base pair contents, the distribution of variant sites, the transition to transversion ratio and different estimates of intra-specific variation and inter-specific variation. Aprioristic hypotheses on factors influencing the molecular drive process and the rates and biases of concerted evolution can be tested with this program. Additionally, satDNA Analyzer generates an output file containing a sequence alignment without shared polymorphisms to be used for further evolutionary analysis by using different phylogenetic softwares.

AVAILABILITY

satDNA Analyzer is freely available at http://satdna.sourceforge.net/. satDNA Analyzer has been designed to operate on Windows, Linux and Mac OS X.

R. Navajas-Pérez current address: Plant Genome Mapping Laboratory, Center for Applied Genetic Technologies, Univ. of Georgia, Athens, GA.

Associate Editor: Nikolaus Rajewsky

Received on October 30, 2006; revised on January 8, 2007; accepted on January 11, 2007

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