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Protocols

MITOS specifications

Information


Unique identifier OMICS_17583
Name MITOS
Interface Web user interface
Restrictions to use None
Input data The genome to be annotated and the appropriate genetic code.
Input format FASTA
Output format BED, GFF, FASTA, and TBL
Computer skills Basic
Version 2.0
Stability Beta
Maintained Yes

Documentation


Maintainer


  • person_outline Matthias Bernt

Publication for MITOS

MITOS citations

 (222)
library_books

The mitochondrial genome of the oribatid mite Paraleius leontonychus: new insights into tRNA evolution and phylogenetic relationships in acariform mites

2018
Sci Rep
PMCID: 5954100
PMID: 29765106
DOI: 10.1038/s41598-018-25981-w

[…] Thr, tRNATrp->tRNASer2, tRNASer2->tRNATrp) based on MFE values (Fig. ). In our study, we could confirm the prediction of these tRNAs and could add four additional ones, mainly based on predictions by MITOS2.Nevertheless, our data suggest that besides three other sarcoptiform species, the two available oribatid mt genomes have a reduced set of tRNAs. Both oribatid species have lost tRNATyr as well […]

call_split

Complete mitochondrial and rDNA complex sequences of important vector species of Biomphalaria, obligatory hosts of the human infecting blood fluke, Schistosoma mansoni

2018
Sci Rep
PMCID: 5943310
PMID: 29743617
DOI: 10.1038/s41598-018-25463-z
call_split See protocol

[…] anually checked for consistency. To check read support consistency, reads were mapped to final assembled mitogenomes and visualized using Integrated Genome Viewer.Mitogenome annotation was done using MITOS2 that includes the latest protein identification model,. We used two references in MITOS2, RefSeq63 Metazoa and RefSeq81 Metazoa, to annotate the mitogenomes for verification and confirmation, e […]

library_books

Extensive gene rearrangements in the mitochondrial genomes of two egg parasitoids, Trichogramma japonicum and Trichogramma ostriniae (Hymenoptera: Chalcidoidea: Trichogrammatidae)

2018
Sci Rep
PMCID: 5935716
PMID: 29728615
DOI: 10.1038/s41598-018-25338-3

[…] urce = Mito/Chloromast, and genetic code = Invertebrate Mito. Twenty of the 22 typical animal mitochondrial tRNA genes were identified. The remaining two tRNA and two rRNA genes were confirmed by the MITOS WebServer using invertebrate mitochondrial genetic code (http://mitos.bioinf.uni-leipzig.de/index.py) (Bernt et al., 2013). ORFinder (http://www.ncbi.nlm.nih.gov/gorf/orfig.cgi) was used to iden […]

call_split

Characterization of the complete mitochondrial DNA of Theretra japonica and its phylogenetic position within the Sphingidae (Lepidoptera, Sphingidae)

2018
Zookeys
PMCID: 5945705
PMID: 29755260
DOI: 10.3897/zookeys.754.23404
call_split See protocol

[…] The overlapping fragments were assembled into a complete linear mitochondria DNA sequence using the DNAStar package (DNAStar Inc. Madison, WI, USA), and the mitogenome was annotated using MITOS2 (). The PCGs and ribosomal RNA (rRNA) genes were verified by NCBI BLAST. The transfer RNA (tRNA) genes were verified by tRNAscan-SE2.0 (; ). Barcoding analysis was performed in Bold Systems v4 […]

call_split

Comparative analyses of the complete mitochondrial genomes of Dosinia clams and their phylogenetic position within Veneridae

2018
PLoS One
PMCID: 5931646
PMID: 29718949
DOI: 10.1371/journal.pone.0196466
call_split See protocol

[…] ere annotated by using NCBI ORF Finder (https://www.ncbi.nlm.nih.gov/orffinder/) and BLASTx with the invertebrate mitochondrial code. The positions of tRNA genes were determined by ARWEN v.1.2 [] and MITOS Web Server []; and secondary structures of tRNAs were inferred using MITOS in default search mode. The rRNA genes were identified by BLAST searches (http://www.ncbi.nlm.nih.gov/BLAST/), the boun […]

library_books

Genome sequencing of Rhinorhipus Lawrence exposes an early branch of the Coleoptera

2018
Front Zool
PMCID: 5930637
PMID: 29743928
DOI: 10.1186/s12983-018-0262-0

[…] ome of R. tamborinensis was identified by a Blast match to a cox1 sequence obtained from the same specimen by PCR-Sanger sequencing. The mitochondrial genome was annotated using gene predictions with MITOS [] and manually refined in Geneious (GenBank Accession Number KT825140).Total genomic DNA of R. tamborinensis was shotgun sequenced with Illumina X Ten platform (Illumina Inc., San Diego, CA) fo […]

Citations

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MITOS institution(s)
Parallel Computing and Complex Systems Group, Department of Computer Science, University Leipzig, Leipzig, Germany; Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, Universität Leipzig, Leipzig, Germany; Zentrum fur Molekulare Biodiversitatsforschung, Zoologisches Forschungsmuseum Alexander Koenig, Bonn, Germany; Max-Planck-Institute for Mathematics in the Sciences, Leipzig, Germany; Fraunhofer Institut fur Zelltherapie und Immunologie, Leipzig, Germany; Department of Theoretical Chemistry University of Vienna, Wien, Austria; Santa Fe Institute, Santa Fe, NM, USA; Architecture et Reactivite de l’ARN, Université de Strasbourg, CNRS, IBMC, Strasbourg, France
MITOS funding source(s)
Supported by the Deutsche Forschungsgemeinschaft [SPP-1174 – Deep Metazoan Phylogeny projects STA 850/2 and STA 850/3-2], Centre National de la Recherche Scientifique (CNRS), Universite de Strasbourg, Association Française contre les Myopathies (MNM1 2009), ANR MITOMOT (ANR-09-BLAN-0091-01), French-German PROCOPE program (DAAD D/0628236, EGIDE PHC 14770PJ), French-German University (DFH-UFA, Cotutelle de these CT-08-10); doctoral fellowship of the German Academic Exchange Service (DAAD D/10/43622), bridge scholarship of the College Doctoral Europeen (CDE), Universite de Strasbourg and an NSC Taiwan Fellowship of the Alexander von Humboldt Foundation.

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