Bioinformatics methods for the comparative analysis of metazoan mitochondrial genome sequences

被引：24

作者：

Bernt, Matthias ^{[1
]}

Braband, Anke ^{[2
]}

Middendorf, Martin ^{[1
]}

Misof, Bernhard ^{[3
]}

Rota-Stabelli, Omar ^{[4
]}

Stadler, Peter F. ^{[5
,6
,7
,8
,9
]}

机构：

[1] Univ Leipzig, Dept Comp Sci, Parallel Comp & Complex Syst Grp, D-04109 Leipzig, Germany

[2] LGC Genom GmbH, D-12459 Berlin, Germany

[3] Zool Forsch Museum Alexander Koenig, D-53113 Bonn, Germany

[4] Fdn Edmund Mach, IASMA Res & Innovat Ctr, Sustainable Agroecosyst & Bioresources Dept, I-38010 San Michele All Adige, TN, Italy

[5] Univ Leipzig, Interdisciplinary Ctr Bioinformat, Bioinformat Grp, Dept Comp Sci, D-04107 Leipzig, Germany

[6] Max Planck Inst Math Sci, D-04103 Leipzig, Germany

[7] Fraunhofer Inst Zelltherapie & Immunol, D-04103 Leipzig, Germany

[8] Univ Vienna, Dept Theoret Chem, A-1090 Vienna, Austria

[9] Santa Fe Inst, Santa Fe, NM 87501 USA

来源：

MOLECULAR PHYLOGENETICS AND EVOLUTION | 2013年 / 69卷 / 02期

关键词：

Bioinformatics; Mitochondria; Genome rearrangements; Substitution models; Gene annotation; AMINO-ACID SUBSTITUTION; PROTEIN-CODING GENES; TRANSFER-RNA GENES; PHYLOGENETIC INFERENCE; WEIGHTED REVERSALS; COMMON ORIGIN; MODEL; DATABASE; EVOLUTION; DNA;

D O I：

10.1016/j.ympev.2012.09.019

中图分类号：

Q5 [生物化学]; Q7 [分子生物学];

学科分类号：

071010 ; 081704 ;

摘要：

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. (C) 2012 Elsevier Inc. All rights reserved.

引用

页码：320 / 327

页数：8

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