Prodigal: Prokaryotic gene recognition and translation initiation site identification

BMC Bioinformatics

Volumn 11, Issue , 2010, Pages

  Hyatt, Doug ^a,b   Chen, Gwo Liang ^a   LoCascio, Philip F ^a   Land, Miriam L ^a   Larimer, Frank W ^a,b   Hauser, Loren J ^a  

^a OAK RIDGE NATIONAL LABORATORY   (United States)

^b UNIVERSITY OF TENNESSEE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

FALSE POSITIVE; GENE PREDICTION; GENE RECOGNITION; GENE STRUCTURE PREDICTION; OPEN SOURCES; TRANSLATION INITIATION SITE;

ALGORITHMS; DNA SEQUENCES; FORECASTING;

GENES;

PROKARYOTA;

ALGORITHM; ARTICLE; BACTERIAL GENOME; COMPUTER PROGRAM; GENETIC DATABASE; GENETICS; PROKARYOTIC CELL; RNA TRANSLATION;

ALGORITHMS; DATABASES, GENETIC; GENOME, BACTERIAL; PEPTIDE CHAIN INITIATION, TRANSLATIONAL; PROKARYOTIC CELLS; SOFTWARE;

EID: 77952299957     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-11-119     Document Type: Article

References (19)

1. Delcher A, Bratke K, Powers E, Salzberg S. Identifying bacterial genes and endosymbiont DNA with Glimmer. Bioinformatics 2007, 23(6):673-679. 10.1093/bioinformatics/btm009, 2387122, 17237039.
2. Lukashin A, Borodovsky M. GeneMark.hmm: new solutions for gene finding. Nucleic Acids Res 1998, 26(4):1107-1115. 10.1093/nar/26.4.1107, 147337, 9461475.
3. Benson D, Karsch-Mizrachi I, Lipman D, Ostell J, Sayers E. GenBank. Nucleic Acids Res 2009, (37 Database):D26-31. 10.1093/nar/gkn723, 2686462, 18940867.
4. Larsen T, Krogh A. EasyGene--a prokaryotic gene finder that ranks ORFs by statistical significance. BMC Bioinformatics 2003, 4:21. 10.1186/1471-2105-4-21, 521197, 12783628.
5. Zhu H, Hu G, Yang Y, Wang J, She Z. MED: a new non-supervised gene prediction algorithm for bacterial and archaeal genomes. BMC Bioinformatics 2007, 8:97. 10.1186/1471-2105-8-97, 1847833, 17367537.
6. Ou H, Guo F, Zhang C. GS-Finder: a program to find bacterial gene start sites with a self-training method. Int J Biochem Cell Biol 2004, 36(3):535-544. 10.1016/j.biocel.2003.08.013, 14687930.
7. Tech M, Pfeifer N, Morgenstern B, Meinicke P. TICO: a tool for improving predictions of prokaryotic translation initiation sites. Bioinformatics 2005, 21(17):3568-3569. 10.1093/bioinformatics/bti563, 15994191.
8. Hu G, Zheng X, Zhu H, She Z. Prediction of translation initiation site for microbial genomes with TriTISA. Bioinformatics 2009, 25(1):123-125. 10.1093/bioinformatics/btn576, 19015130.
9. Altschul S, Gish W, Miller W, Myers E, Lipman D. Basic local alignment search tool. J Mol Biol 1990, 215(3):403-410.
10. VerBerkmoes N, Shah M, Lankford P, Pelletier D, Strader M, Tabb D, McDonald W, Barton J, Hurst G, Hauser L, et al. Determination and comparison of the baseline proteomes of the versatile microbe Rhodopseudomonas palustris under its major metabolic states. J Proteome Res 2006, 5(2):287-298. 10.1021/pr0503230, 16457594.
11. Badger J, Olsen G. CRITICA: coding region identification tool invoking comparative analysis. Mol Bio Evol 1999, 16(4):512-24.
12. Rudd K. EcoGene: a genome sequence database for Escherichia coli K-12. Nucleic Acids Res 2000, 28(1):60-64. 10.1093/nar/28.1.60, 102481, 10592181.
13. Rutherford K, Parkhill J, Crook J, Horsnell T, Rice P, Rajandream M, Barrell B. Artemis: sequence visualization and annotation. Bioinformatics 2000, 16(10):944-5. 10.1093/bioinformatics/16.10.944, 11120685.
14. Bellman R. On the Theory of Dynamic Programming. Proc Natl Acad Sci USA 1952, 38(8):716-719. 10.1073/pnas.38.8.716, 1063639, 16589166.
15. Shine J, Dalgarno L. Terminal-sequence analysis of bacterial ribosomal RNA. Correlation between the 3'-terminal-polypyrimidine sequence of 16-S RNA and translational specificity of the ribosome. Eur J Biochem 1975, 57(1):221-230. 10.1111/j.1432-1033.1975.tb02294.x, 809282.
16. Dam P, Olman V, Harris K, Su Z, Xu Y. Operon prediction using both genome-specific and general genomic information. Nucleic Acids Res 2007, 35(1):288-98. 10.1093/nar/gkl1018, 1802555, 17170009.
17. Aivaliotis M, Gevaert K, Falb M, Tebbe A, Konstantinidis K, Bisle B, Klein C, Martens L, Staes A, Timmerman E, et al. Large-scale identification of N-terminal peptides in the halophilic archaea Halobacterium salinarum and Natronomonas pharaonis. J Proteome Res 2007, 6(6):2195-2204. 10.1021/pr0700347, 17444671.
18. Hu G, Zheng X, Yang Y, Ortet P, She Z, Zhu H. ProTISA: a comprehensive resource for translation initiation site annotation in prokaryotic genomes. Nucleic Acids Res 2008, (36 Database):D114-119. 2238952, 17942412.
19. Gattiker A, Dessimoz C, Schneider A, Xenarios I, Pagni M, Rougemont J. The Microbe browser for comparative genomics. Nucleic Acids Res 2009, (37 Web server):W296-9. 10.1093/nar/gkp268, 2703916, 19406928.