title: Bioinformatics methods for the comparative analysis of metazoan mitochondrial genome sequences.
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.
authors.affiliation: Parallel Computing and Complex Systems Group, Department of Computer Science, University of Leipzig, Augustusplatz 10, D-04109 Leipzig, Germany. Electronic address: bernt@informatik.uni-leipzig.de.
authors.forename: Matthias
authors.initials: M
authors.lastname: Bernt
authors.forename: Anke
authors.initials: A
authors.lastname: Braband
authors.forename: Martin
authors.initials: M
authors.lastname: Middendorf
authors.forename: Bernhard
authors.initials: B
authors.lastname: Misof
authors.forename: Omar
authors.initials: O
authors.lastname: Rota-Stabelli
authors.forename: Peter F
authors.initials: PF
authors.lastname: Stadler
mesh_terms: D000818:Animals; D019295:Computational Biology / Q000379:methods*; D030541:Databases, Genetic; D019143:Evolution, Molecular; D023061:Gene Order; D015321:Gene Rearrangement; D054629:Genome, Mitochondrial; D008957:Models, Genetic; D058977:Molecular Sequence Annotation; D010802:Phylogeny; D012335:RNA, Ribosomal / Q000235:genetics; D012343:RNA, Transfer / Q000235:genetics; D017422:Sequence Analysis, DNA / Q000379:methods*
chemical_list: D012335:RNA, Ribosomal; D012343:RNA, Transfer