SatDNA Analyzer: a computing tool for satellite-DNA evolutionary analysis.
Bioinformatics
; 23(6): 767-8, 2007 Mar 15.
Article
em En
| MEDLINE
| ID: mdl-17242030
ABSTRACT
UNLABELLED 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. 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.
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Base de dados:
MEDLINE
Assunto principal:
Software
/
DNA Satélite
/
Análise Mutacional de DNA
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Alinhamento de Sequência
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Análise de Sequência de DNA
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Evolução Molecular
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Polimorfismo de Nucleotídeo Único
Idioma:
En
Ano de publicação:
2007
Tipo de documento:
Article