title: MITOS: improved de novo metazoan mitochondrial genome annotation.
abstract: About 2000 completely sequenced mitochondrial genomes are available from the NCBI RefSeq 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.
authors.affiliation: Parallel Computing and Complex Systems Group, Department of Computer Science, University Leipzig, Augustusplatz 10-11, 04109 Leipzig, Germany. Electronic address: bernt@informatik.uni-leipzig.de.
authors.forename: Matthias
authors.initials: M
authors.lastname: Bernt
authors.forename: Alexander
authors.initials: A
authors.lastname: Donath
authors.forename: Frank
authors.initials: F
authors.lastname: Jühling
authors.forename: Fabian
authors.initials: F
authors.lastname: Externbrink
authors.forename: Catherine
authors.initials: C
authors.lastname: Florentz
authors.forename: Guido
authors.initials: G
authors.lastname: Fritzsch
authors.forename: Joern
authors.initials: J
authors.lastname: Pütz
authors.forename: Martin
authors.initials: M
authors.lastname: Middendorf
authors.forename: Peter F
authors.initials: PF
authors.lastname: Stadler
mesh_terms: D000818:Animals; D019295:Computational Biology; D019143:Evolution, Molecular; D054629:Genome, Mitochondrial; D020407:Internet; D058977:Molecular Sequence Annotation; D010802:Phylogeny; D017422:Sequence Analysis, DNA; D012984:Software