title: MitoFish and MitoAnnotator: a mitochondrial genome database of fish with an accurate and automatic annotation pipeline.
abstract: Mitofish is a database of fish mitochondrial genomes (mitogenomes) that includes powerful and precise de novo annotations for mitogenome sequences. Fish occupy an important position in the evolution of vertebrates and the ecology of the hydrosphere, and mitogenomic sequence data have served as a rich source of information for resolving fish phylogenies and identifying new fish species. The importance of a mitogenomic database continues to grow at a rapid pace as massive amounts of mitogenomic data are generated with the advent of new sequencing technologies. A severe bottleneck seems likely to occur with regard to mitogenome annotation because of the overwhelming pace of data accumulation and the intrinsic difficulties in annotating sequences with degenerating transfer RNA structures, divergent start/stop codons of the coding elements, and the overlapping of adjacent elements. To ease this data backlog, we developed an annotation pipeline named MitoAnnotator. MitoAnnotator automatically annotates a fish mitogenome with a high degree of accuracy in approximately 5 min; thus, it is readily applicable to data sets of dozens of sequences. MitoFish also contains re-annotations of previously sequenced fish mitogenomes, enabling researchers to refer to them when they find annotations that are likely to be erroneous or while conducting comparative mitogenomic analyses. For users who need more information on the taxonomy, habitats, phenotypes, or life cycles of fish, MitoFish provides links to related databases. MitoFish and MitoAnnotator are freely available at http://mitofish.aori.u-tokyo.ac.jp/ (last accessed August 28, 2013); all of the data can be batch downloaded, and the annotation pipeline can be used via a web interface.
authors: Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwa, Chiba, Japan.
authors: Wataru
authors: W
authors: Iwasaki
authors: Tsukasa
authors: T
authors: Fukunaga
authors: Ryota
authors: R
authors: Isagozawa
authors: Koichiro
authors: K
authors: Yamada
authors: Yasunobu
authors: Y
authors: Maeda
authors: Takashi P
authors: TP
authors: Satoh
authors: Tetsuya
authors: T
authors: Sado
authors: Kohji
authors: K
authors: Mabuchi
authors: Hirohiko
authors: H
authors: Takeshima
authors: Masaki
authors: M
authors: Miya
authors: Mutsumi
authors: M
authors: Nishida
mesh_terms: D000818:Animals; D030541:Databases, Genetic; D019143:Evolution, Molecular; D005399:Fishes / Q000235:genetics*; D054629:Genome, Mitochondrial; D023281:Genomics; D059014:High-Throughput Nucleotide Sequencing; D058977:Molecular Sequence Annotation / Q000379:methods*; D010802:Phylogeny; D012343:RNA, Transfer / Q000235:genetics; D012984:Software
chemical_list: D012343:RNA, Transfer
keywords: database; fish; genome annotator; high-throughput sequencing; mitochondrion; phylogenetics
references: Mol Phylogenet Evol. 2000 Dec;17(3):437-55
references: 11133198
references: Nature. 1981 Apr 9;290(5806):457-65
references: 7219534
references: J Mol Evol. 1991 Feb;32(2):153-61
references: 1706782
references: Nucleic Acids Res. 2012 Jan;40(Database issue):D130-5
references: 22121212
references: Nucleic Acids Res. 2012 Apr;40(7):2833-45
references: 22139921
references: Nucleic Acids Res. 1999 Apr 15;27(8):1767-80
references: 10101183
references: Bioinformatics. 2004 Nov 22;20(17):3252-5
references: 15180927
references: Mol Biol Evol. 2003 Nov;20(11):1917-24
references: 12949142
references: Bioinformatics. 2008 Jan 15;24(2):172-5
references: 18033792
references: Nucleic Acids Res. 1980 Nov 25;8(22):5207-12
references: 6906661
references: Bioinformatics. 2009 May 15;25(10):1335-7
references: 19307242
references: Nucleic Acids Res. 2009 Jan;37(Database issue):D946-50
references: 18953030
references: Cell. 1980 Nov;22(2 Pt 2):393-403
references: 7448867
references: BMC Bioinformatics. 2009 Dec 15;10:421
references: 20003500
references: Mol Phylogenet Evol. 2003 Jan;26(1):121-38
references: 12470944
references: Mol Biol Evol. 2011 Jun;28(6):1927-42
references: 21242529
references: Mol Phylogenet Evol. 2003 Jan;26(1):110-20
references: 12470943
references: Proc Natl Acad Sci U S A. 2002 Jun 11;99(12):8151-6
references: 12034869
references: Bioinformatics. 2006 Apr 1;22(7):902-3
references: 16446277
references: J Mol Evol. 1989 Sep;29(3):202-7
references: 2506356
references: Mol Phylogenet Evol. 2013 Nov;69(2):313-9
references: 22982435
references: Bioinformatics. 2005 May 15;21(10):2566-7
references: 15713730
references: Nucleic Acids Res. 1997 Mar 1;25(5):955-64
references: 9023104
references: J Mol Evol. 2004 Sep;59(3):287-97
references: 15553084
references: BMC Genomics. 2011 Jan 14;12:35
references: 21235758
references: Nucleic Acids Res. 2012 Jan;40(Database issue):D1168-72
references: 22123747
references: PLoS One. 2013 Sep 04;8(9):e73535
references: 24023883
references: Nucleic Acids Res. 1980 Nov 25;8(22):5213-22
references: 6906662
references: Nucleic Acids Res. 2013 Jan;41(Database issue):D36-42
references: 23193287
references: Heredity (Edinb). 2008 Oct;101(4):301-20
references: 18612321
references: Mol Ecol Notes. 2007 May 1;7(3):355-364
references: 18784790
references: Mar Biotechnol (NY). 1999 Sep;1(5):416-0426
references: 10525676