MITOS: Improved de novo metazoan mitochondrial genome annotation

被引：3867

作者：

Bernt, Matthias ^{[1
]}

Donath, Alexander ^{[2
,3
,4
]}

Juehling, Frank ^{[2
,3
,9
]}

Externbrink, Fabian ^{[1
,2
,3
]}

Florentz, Catherine ^{[9
]}

Fritzsch, Guido ^{[2
,3
]}

Puetz, Joern ^{[9
]}

Middendorf, Martin ^{[1
]}

Stadler, Peter F. ^{[2
,3
,5
,6
,7
,8
]}

机构：

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

[2] Univ Leipzig, Bioinformat Grp, Dept Comp Sci, D-04107 Leipzig, Germany

[3] Univ Leipzig, Interdisciplinary Ctr Bioinformat, D-04107 Leipzig, Germany

[4] Zool Forsch Museum Alexander Koenig, Zentrum Mol Biodivers Forsch, D-53113 Bonn, Germany

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

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

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

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

[9] Univ Strasbourg, CNRS, IBMC, F-67084 Strasbourg, France

来源：

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

关键词：

Metazoa; Mitochondria; Genome; Annotation; Server; TRANSFER-RNA GENE; EVOLUTION; DUPLICATION; NUCLEOTIDE; INSIGHTS; DATABASE; PROGRAM;

D O I：

10.1016/j.ympev.2012.08.023

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：

About 2000 completely sequenced mitochondrial genomes are available from the NCBI Re fSeq data base together with manually curated annotations of their protein-coding genes, rRNAs, and tRNAs. This annotation information, which has accumulated over two decades, has been obtained with a diverse set of computational tools and annotation strategies. Despite all efforts of manual curation it is still plagued by misassignments of reading directions, erroneous gene names, and missing as well as false positive annotations in particular for the RNA genes. Taken together, this causes substantial problems for fully automatic pipelines that aim to use these data comprehensively for studies of animal phylogenetics and the molecular evolution of mitogenomes. The MITOS pipeline is designed to compute a consistent de novo annotation of the mitogenomic sequences. We show that the results of MITOS match RefSeq and MitoZoa in terms of annotation coverage and quality. At the same time we avoid biases, inconsistencies of nomenclature, and typos originating from manual curation strategies. The MITOS pipeline is accessible online at http://mitos.bioinf.uni-leipzig.de. (C) 2012 Elsevier Inc. All rights reserved.

引用

页码：313 / 319

页数：7

共 34 条

[31] ANIMAL MITOCHONDRIAL-DNA - STRUCTURE AND EVOLUTION [J].

WOLSTENHOLME, DR .

INTERNATIONAL REVIEW OF CYTOLOGY-A SURVEY OF CELL BIOLOGY, 1992, 141 :173-216

[32] The European ribosomal RNA database [J].

Wuyts, J ;

Perrière, G ;

Van de Peer, Y .

NUCLEIC ACIDS RESEARCH, 2004, 32 :D101-D103

[33] Automatic annotation of organellar genomes with DOGMA [J].

Wyman, SK ;

Jansen, RK ;

Boore, JL .

BIOINFORMATICS, 2004, 20 (17) :3252-3255

[34] The complete mitochondrial genome of Setaria digitata (Nematoda: Filarioidea): Mitochondrial gene content, arrangement and composition compared with other nematodes [J].

Yatawara, Lalani ;

Wickramasinghe, Susiji ;

Rajapakse, R. P. V. J. ;

Agatsuma, Takeshi .

MOLECULAR AND BIOCHEMICAL PARASITOLOGY, 2010, 173 (01) :32-38

← 1 2 3 4 →