GenePRIMP: A gene prediction improvement pipeline for prokaryotic genomes

Nature Methods

Volumn 7, Issue 6, 2010, Pages 455-457

  Pati, Amrita ^a   Ivanova, Natalia N ^a   Mikhailova, Natalia ^a   Ovchinnikova, Galina ^a   Hooper, Sean D ^a,b   Lykidis, Athanasios ^a   Kyrpides, Nikos C ^a  

^a DOE JOINT GENOME INSTITUTE   (United States)

^b UPPSALA UNIVERSITY   (Sweden)

Author keywords

[No Author keywords available]

Indexed keywords

AB INITIO CALCULATION; ARCHAEBACTERIUM; ARTICLE; BACTERIAL GENOME; COMPUTER PREDICTION; CONTROLLED STUDY; DNA BASE COMPOSITION; GENOMICS; METHANOSPHAERULA PALUSTRIS; MYCOBACTERIUM; NONHUMAN; PRIORITY JOURNAL; SEQUENCE ANALYSIS; TRANSCRIPTION INITIATION SITE;

COMPUTATIONAL BIOLOGY; GENOME, ARCHAEAL; GENOME, BACTERIAL; MODELS, GENETIC;

PROKARYOTA;

EID: 77953023066     PISSN: 15487091     EISSN: 15491676     Source Type: Journal    
DOI: 10.1038/nmeth.1457     Document Type: Article

References (15)

1. Benson, D.A., Karsch-Mizrachi, I., Lipman, D.J., Ostell, J. & Sayers, E.W. Nucleic Acids Res. 38, D46-D51 (2010).
2. Ishino, Y., Okada, H., Ikeuchi, M. & Taniguchi, H. Proteomics 7, 4053-4065 (2007).
3. Smollett, K.L. et al. Microbiology 155, 186-197 (2009).
4. Kyrpides, N.C. Nat. Biotechnol. 27, 627-632 (2009).
5. Hyatt, D. et al. BMC Bioinformatics (in the press).
6. Besemer, J., Lomsadze, A. & Borodovsky, M. Nucleic Acids Res. 29, 2607-2618 (2001).
7. Delcher, A.L., Bratke, K.A., Powers, E.C. & Salzberg, S.L. Bioinformatics 23, 673-679 (2007).
8. Zhu, H.Q., Hu, G.Q., Quyang, Z.Q., Wang, J. & She, Z.S. Bioinformatics 20, 3308-3317 (2004).
9. Tech, M. & Meinicke, P. BMC Bioinformatics 7, 121 (2006).
10. Yu, G.X. et al. Nucleic Acids Res. 35, 3953-3962 (2007).
11. Nagy, A. et al. BMC Bioinformatics 9, 353 (2008).
12. Castellana, N.E. et al. Proc. Natl. Acad. Sci. USA 105, 21034-21038 (2008).
13. Markowitz, V.M. et al. Nucleic Acids Res. 38, D382-D390 (2010).
14. Aziz, R.K. et al. BMC Genomics 9, 75 (2008).
15. Bocs, S., Cruveiller, S., Vallenet, D., Nuel, G. & Medigue, C. Nucleic Acids Res. 31, 3723-3726 (2003).