MITOS: Improved de novo metazoan mitochondrial genome annotation
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Altschul, 1990, Basic local alignment search tool, J. Mol. Biol., 215, 403, 10.1016/S0022-2836(05)80360-2
Beagley, 1996, Two mitochondrial group I introns in a metazoan, the sea anemone Metridium senile: one intron contains genes for subunits 1 and 3 of NADH dehydrogenase, Proc. Natl. Acad. Sci. USA, 93, 5619, 10.1073/pnas.93.11.5619
Bernt, 2013, Bioinformatics methods for the comparative analysis of metazoan mitochondrial genome sequences, Mol. Phyl. Evol., 69, 320, 10.1016/j.ympev.2013.05.002
Bernt, 2013, Genetic aspects of mitochondrial genome evolution, Mol. Phyl. Evol., 69, 328, 10.1016/j.ympev.2012.10.020
Boore, J.L., 2001. Mitochondrial genome rearrangement guide. Version 6.1.
Boore, 2006, Requirements and standards for organelle genome databases, OMICS, 10, 119, 10.1089/omi.2006.10.119
Boore, 2005, Sequencing and comparing whole mitochondrial genomes of animals, Method Enzymol., 395, 311, 10.1016/S0076-6879(05)95019-2
Breton, 2010, Novel protein genes in animal mtDNA: a new sex determination system in freshwater mussels (Bivalvia: Unionoida)?, Mol. Biol. Evol., 28, 1645, 10.1093/molbev/msq345
Cock, 2009, Biopython: freely available python tools for computational molecular biology and bioinformatics, Bioinformatics, 25, 1422, 10.1093/bioinformatics/btp163
Dellaporta, 2006, Mitochondrial genome of Trichoplax adhaerens supports placozoa as the basal lower metazoan phylum, Proc. Natl. Acad. Sci. USA, 103, 8751, 10.1073/pnas.0602076103
Eddy, 1994, RNA sequence analysis using covariance models, Nucl. Acids Res., 22, 2079, 10.1093/nar/22.11.2079
Feijao, 2006, AMiGA: the arthropodan mitochondrial genomes accessible database, Bioinformatics, 22, 902, 10.1093/bioinformatics/btl021
Fujita, 2007, Multiple origins and rapid evolution of duplicated mitochondrial genes in parthenogenetic geckos (Heteronotia binoei; Squamata, Gekkonidae), Mol. Biol. Evol., 24, 2775, 10.1093/molbev/msm212
Jameson, 2003, OGRe: a relational database for comparative analysis of mitochondrial genomes, Nucl. Acids Res., 31, 202, 10.1093/nar/gkg077
Jühling, 2012, Improved systematic tRNA gene annotation allows new insights into the evolution of mitochondrial tRNA structures and into the mechanisms of mitochondrial genome rearrangements, Nucl. Acids Res., 40, 2833, 10.1093/nar/gkr1131
Laslett, 2008, ARWEN: a program to detect tRNA genes in metazoan mitochondrial nucleotide sequences, Bioinformatics, 24, 172, 10.1093/bioinformatics/btm573
Lavrov, 2005, Mitochondrial genomes of two demosponges provide insights into an early stage of animal evolution, Mol. Biol. Evol., 22, 1231, 10.1093/molbev/msi108
Lavrov, 2005, Transfer RNA gene recruitment in mitochondrial DNA, Trends Genet., 21, 129, 10.1016/j.tig.2005.01.004
Lowe, 1997, tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence, Nucl. Acids Res., 25, 955, 10.1093/nar/25.5.0955
Lupi, 2010, MitoZoa: a curated mitochondrial genome database of metazoans for comparative genomics studies, Mitochondrion, 10, 192, 10.1016/j.mito.2010.01.004
Mindell, 1998, An extra nucleotide is not translated in mitochondrial ND3 of some birds and turtles, Mol. Biol. Evol., 15, 1568, 10.1093/oxfordjournals.molbev.a025884
Nawrocki, 2009, Infernal 1.0: inference of RNA alignments, Bioinformatics, 25, 1335, 10.1093/bioinformatics/btp157
Pruitt, 2007, NCBI reference sequences (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins, Nucl. Acids Res., 35, D61, 10.1093/nar/gkl842
Rawlings, 2003, Changing identities: tRNA duplication and remolding within animal mitochondrial genomes, Proc. Natl. Acad. Sci. USA, 100, 15700, 10.1073/pnas.2535036100
Saks, 1998, Evolution of a transfer RNA gene through a point mutation in the anticodon, Science, 279, 1665, 10.1126/science.279.5357.1665
SanMauro, 2006, A hotspot of gene order rearrangement by tandem duplication and random loss in the vertebrate mitochondrial genome, Mol. Biol. Evol., 23, 227, 10.1093/molbev/msj025
Sheffield, 2010, Mitochondrial genomics in Orthoptera using MOSAS, Mitochondr. DNA, 21, 87, 10.3109/19401736.2010.500812
Wang, 2008, Seventeen new complete mtDNA sequences reveal extensive mitochondrial genome evolution within the Demospongiae, PLoS ONE, 3, e2723, 10.1371/journal.pone.0002723
Wang, 2011, Gene recruitment a common mechanism in the evolution of transfer RNA gene families, Gene, 475, 22, 10.1016/j.gene.2010.12.009
Wolstenholme, 1992, Animal mitochondrial DNA: structure and evolution, Int. Rev. Cytol., 141, 173, 10.1016/S0074-7696(08)62066-5
Wyman, 2004, Automatic annotation of organellar genomes with DOGMA, Bioinformatics, 20, 3252, 10.1093/bioinformatics/bth352