Automatic annotation of organellar genomes with DOGMA

Bioinformatics

Volumn 20, Issue 17, 2004, Pages 3252-3255

  Wyman, Stacia K ^a   Jansen, Robert K ^b   Boore, Jeffrey L ^c  

^a University of Texas at Austin ^*  (United States)

^b UNIVERSITY OF TEXAS AT AUSTIN   (United States)

^c DOE JOINT GENOME INSTITUTE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

MESSENGER RNA; TRANSFER RNA;

ARTICLE; AUTOMATION; BASE PAIRING; CELL ORGANELLE; CHLOROPLAST; COMPUTER INTERFACE; DATA BASE; GENBANK; GENE IDENTIFICATION; GENOME; MITOCHONDRION; NONHUMAN; PRESSURE WAVE; PRIORITY JOURNAL; PROTEIN SECONDARY STRUCTURE;

ANIMALIA;

EID: 10244240599     PISSN: 13674803     EISSN: 13674811     Source Type: Journal    
DOI: 10.1093/bioinformatics/bth352     Document Type: Article

References (12)

1. Altschul,S., Gish,W., Miller,W., Myers,E. and Lipman,D. (1990) Basic local alignment search tool. J. Mol. Biol., 215, 403-410.
2. Boore,J. (1999) Animal mitochondrial genomes. Nucleic Acids Res., 27, 1767-1780.
3. Boore,J. (2000) The duplication/random loss model for gene rearrangement exemplified by mitochondrial genomes of deuterostome animals. In Sankoff,D. and Nadeau,J. (eds), Comparative Genomics. Vol. 1, Kluwer Academic Publisher, Dordrecht, The Netherlands, pp. 133-147.
4. Boore,J. and Brown,W. (1998) Big trees from little genomes: mitochondrial gene order as a phylogenetic tool. Curr. Opin. Genet. Dev., 8, 668-674.
5. Cao,Y., Fujiwara,M., Nikaido,M., Okada,N. and Hasegawa,M. (2000) Interordinal relationships and timesecale of eutherian evolution as inferred from mitochondrial genome data. Gene, 259, 149-158.
6. Cosner,M., Jansen,R., Palmer,J. and Downie,S. (1997) The highly rearranged chloroplast genome of Trachelium caeruleum (campanulaceae): multiple inversions, inverted repeat expansion and contraction, transposition, insertions/deletions, and several repeat families. Curr Genet., 31, 419-429.
7. Eddy,S. and Durbin,R. (1994) RNA sequence analysis using covariance models. Nucleic Acids Res., 22, 2079-2088.
8. Martin,M., Rujan,T., Richly,T., Hansen,A., Cornelsen,S., Lins,T., Leister,D., Stoebe,B., Hasegawa,M. and Penny,D. (2002) Evolutionary analysis of Arabidopsis, cyanobacterial, and chloroplast genomes reveals plastid phylogeny and thousands of cyanobacterial genes in the nucleus. Proc. Natl Acad. Sci., USA, 99, 12246-12251.
9. Miya,M., Kawaguchi,A. and Nishida,M. (2001) Mitogenomic exploration of higher teleostean phylogenies: a case study for moderate-scale evolutionary genomics with 38 newly determined complete mitochondrial DNA sequences. Mol. Biol. Evol., 18, 1993-2009.
10. Palmer,J. (1991) Plastid chromosomes: structure and evolution. Cell Culture Somatic Cell Genet. Plants, 7A, 5-53.
11. Wallace,D. (1999) Mitochondrial diseases in man and mouse. Science, 283, 482-488.
12. Wyman,S. and Boore,J. (2003) Annotating animal mitochondrial tRNAs: an experimental evaluation of four methods. In Proceedings of European Conference on Computer. Biology, Local Proceedings, Self Published, Paris, France, pp. 44-46.