In this review we provide an overview of various bioinformatics methods and tools for the analysis of metazoan mitochondrial genomes. We compare available dedicated databases and present current tools for accurate genome annotation, identification of protein coding genes, and determination of tRNA and rRNA models.We also evaluate various tools and models for phylogenetic tree inference using gene order or sequence based data. As for gene order based methods, we compare rearrangement based and gene cluster based methods for gene order rearrangement analysis. As for sequence based methods, we give special emphasis to substitution models or data treatment that reduces certain systematic biases that are typical for metazoan mitogenomes such as within genome and/or among lineage compositional heterogeneity

Bernt, M.; Braband, A.; Middendorf, M.; Misof, B.; Rota Stabelli, O.; Stadler, P.F. (2013). Bioinformatics methods for the comparative analysis of metazoan mitochondrial genome sequences. MOLECULAR PHYLOGENETICS AND EVOLUTION, 69 (2): 320-327. doi: 10.1016/j.ympev.2012.09.019 handle: http://hdl.handle.net/10449/22411

Bioinformatics methods for the comparative analysis of metazoan mitochondrial genome sequences

Rota Stabelli, Omar;
2013-01-01

Abstract

In this review we provide an overview of various bioinformatics methods and tools for the analysis of metazoan mitochondrial genomes. We compare available dedicated databases and present current tools for accurate genome annotation, identification of protein coding genes, and determination of tRNA and rRNA models.We also evaluate various tools and models for phylogenetic tree inference using gene order or sequence based data. As for gene order based methods, we compare rearrangement based and gene cluster based methods for gene order rearrangement analysis. As for sequence based methods, we give special emphasis to substitution models or data treatment that reduces certain systematic biases that are typical for metazoan mitogenomes such as within genome and/or among lineage compositional heterogeneity
Bioinformatics
Mitochondria
Genome rearrangements
Substitution models
Gene annotation
Settore BIO/18 - GENETICA
2013
Bernt, M.; Braband, A.; Middendorf, M.; Misof, B.; Rota Stabelli, O.; Stadler, P.F. (2013). Bioinformatics methods for the comparative analysis of metazoan mitochondrial genome sequences. MOLECULAR PHYLOGENETICS AND EVOLUTION, 69 (2): 320-327. doi: 10.1016/j.ympev.2012.09.019 handle: http://hdl.handle.net/10449/22411
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