Evaluation of three automated genome annotations for Halorhabdus utahensis

PLoS ONE

Volumn 4, Issue 7, 2009, Pages

  Bakke, Peter ^a   Carney, Nick ^a   DeLoache, Will ^a   Gearing, Mary ^a   Ingvorsen, Kjeld ^b   Lotz, Matt ^a   McNair, Jay ^a   Penumetcha, Pallavi ^a   Simpson, Samantha ^a   Voss, Laura ^a   Win, Max ^a   Heyer, Laurie J ^a   Campbell, A Malcolm ^a  

^a DAVIDSON COLLEGE   (United States)

^b AARHUS UNIVERSITY   (Denmark)

Author keywords

[No Author keywords available]

Indexed keywords

TRANSFER RNA;

ARTICLE; AUTOMATION; BACTERIAL GENOME; BACTERIAL GROWTH; BINDING SITE; COMPARATIVE STUDY; CONTROLLED STUDY; ENZYME ACTIVITY; GENE REPLICATION; GENE SEQUENCE; GENOME ANALYSIS; HALOPHILIC ARCHAEON; HALORHABDUS UTAHENSIS; INFORMATION PROCESSING; INTRON; NONHUMAN; NUCLEOTIDE SEQUENCE; PROTEIN BINDING; RIBOSOME; SEQUENCE DATABASE; SPECIES DIFFERENCE; ARCHAEAL GENOME; DNA REPLICATION ORIGIN; EVALUATION; GENETICS; HALOBACTERIALES;

ARCHAEA; HALORHABDUS UTAHENSIS;

GENOME, ARCHAEAL; HALOBACTERIACEAE; INTRONS; REPLICATION ORIGIN; RNA, TRANSFER;

EID: 67651091927     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0006291     Document Type: Article

References (25)

1. Eisen JA (2007) Environmental Shotgun Sequencing: Its Potential and Challenges for Studying the Hidden World of Microbes. PLoS Biol 5(3): e82.
2. Hall H (2007) Advanced sequencing technologies and their wider impact in microbiology. The Journal of Experimental Biology 209: 1518-1525.
3. Fumoto M, Miyazaki S, Sugawara H (2002) Genome Information Broker (GIB): data retrieval and comparative analysis system for completed microbial genomes and more. Nucleic Acids Research 30(1): 66-68.
4. Markowitz VM, Korzeniewski F, Palaniappan K, Szeto E, Werner G, et al. (2006) The integrated microbial genomes (IMG) system. Nucleic Acids Research 34: 344-348.
5. Aziz RK, Bartels D, Best AA, Dejongh M, Disz T, et al. (2008) The RAST Server: Rapid Annotation using Subsystems Technology. BMC Genomics 9: 75.
6. Wainø M, Tindall BJ, Ingvorsen K (2000) Halorhabdus utahensis gen. nov., sp. Nov., an aerobic, extremely halophilic member of the Archaea from Great Salt Lake, Utah. International Journal of Systematic and Evolutionary Microbiology 50: 183-190.
7. Ludwig W, Schleifer KH (1994) Bacterial phylogeny based on 16S and 23S rRNA sequence analysis. FEMS Microbiology Reviews 15: 155-173.
8. Jiong M, Campbell A, Karlin S (2002) Correlations between Shine-Dalgarno Sequences and Gene Features Such as Predicted Expression Levels and Operon Structures. Journal of Bacteriology 184: 5733-5745.
9. Shine J, Dalgarno L (1974) The 3′-Terminal Sequence of Escherichia coli 16S Ribosomal RNA: Complementarity to Nonsense Triplets and Ribosome Binding Sites. Proc Nat Acad Sci 71: 1342-1346.
10. Thompson LD, Daniels CJ (1988) A tRNA-trp Intron Endonuclease from Halobacterium Volcanii. The Journal of Biological Chemistry 263: 17951-17959.
11. Berquist BR, DasSarma S (2003) An Archaeal Chromosomal Autonomous Replicating Sequence Element from an Extreme Halophile, Halobacterium sp. Strain NRC-1. Journal of Bacteriology 185: 5959-5966.
12. Duggin IG, Bell SD (2006) The Chromosome Replication Machinery of the Archaeon Sulfolobus solfataricus. J Biol Chem 281: 15029-15302.
13. Grabowski B, Kelman Z (2003) Archaeal DNA Replication: Eukaryal Proteins in a Bacterial Context. Annual Review of Microbiology 57: 487-516.
14. Barry ER, Bell SD (2006) DNA Replication in the Archaea. Microbiol. Mol Biol Rev 70: 876-887.
15. Webb EC (1992) Enzyme Nomenclature 1992: Recommendations of the Nomenclature Committee of the International Union of Biochemistry and Molecular Biology on the Nomenclature and Classification of Enzymes. New York: Academic Press, Inc. pp 884.
16. Aziz RK, Bartels D, Best AA, Dejongh M, Disz T, et al. (2008) The RAST Server: Rapid Annotation using Subsystems Technology. BMC Genomics 9: 75.
17. Lowe TM, Eddy SR (1997) tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res 25: 955-964.
18. Jiong M, Campbell A, Karlin S (2002) Correlations between Shine-Dalgarno Sequences and Gene Features Such as Predicted Expression Levels and Operon Structures. Journal of Bacteriology 184: 5733-5745.
19. Ivanova NN, Mavromatis K, Chen IA, Markowitz VM, Kyrpides NC (2006) Standard Operating Procedure for the Annotations of Genomes and Metagenomes submitted to the Integral Microbial Genomes Expert Review (IMG-ER) System.
20. Aziz RK, Bartels D, Best AA, Dejongh M, Disz T, et al. (2008) The RAST Server: Rapid Annotation using Subsystems Technology. BMC Genomics 9: 75.
21. Aziz RK, Bartels D, Best AA, Dejongh M, Disz T, et al. (2008) The RAST Server: Rapid Annotation using Subsystems Technology. BMC Genomics 9: 75.
22. Overbeek R, Bartels D, Vonstein V, Meyer F (2007) Annotation of Bacterial and Archaeal Genomes: Improving Accuracy and Consistency. Chem Rev 107: 3431-3447.
23. Aziz RK, Bartels D, Best AA, Dejongh M, Disz T, et al. (2008) The RAST Server: Rapid Annotation using Subsystems Technology. BMC Genomics 9: 75.
24. Ingvorsen K, Jørgensen BB (1984) Kinetics of sulfate uptake by freshwater and marine species of Desulfovibrio. Arch Microbiol 139: 61-66.
25. Wainø M, Ingvorsen K (2003) Production of β-xylanase and β-xylosidase by the extremely halophilic archaeon Halorhabdus utahensis. Extremophiles 7: 87-93.