Nucleic Acids Research, Vol 27, Issue 23 4636-4641, Copyright © 1999 by Oxford University Press
AL Delcher, D Harmon, S Kasif, O White and SL Salzberg
The GLIMMER system for microbial gene identification finds approximately
97-98% of all genes in a genome when compared with published annotation.
This paper reports on two new results: (i) significant technical
improvements to GLIMMER that improve its accuracy still further, and (ii) a
comprehensive evaluation that demonstrates that the accuracy of the system
is likely to be higher than previously recognized. A significant proportion
of the genes missed by the system appear to be hypothetical proteins whose
existence is only supported by the predictions of other programs. When the
analysis is restricted to genes that have significant homology to genes in
other organisms, GLIMMER misses <1% of known genes.
ARTICLES
Improved microbial gene identification with GLIMMER
Department of Computer Science, Loyola College in Maryland, Baltimore, MD 21210, USA. delcher@cs.loyola.edu
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D. W. Udwary, L. Zeigler, R. N. Asolkar, V. Singan, A. Lapidus, W. Fenical, P. R. Jensen, and B. S. Moore Genome sequencing reveals complex secondary metabolome in the marine actinomycete Salinispora tropica PNAS, June 19, 2007; 104(25): 10376 - 10381. [Abstract] [Full Text] [PDF]
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C. Geslin, M. Gaillard, D. Flament, K. Rouault, M. Le Romancer, D. Prieur, and G. Erauso Analysis of the First Genome of a Hyperthermophilic Marine Virus-Like Particle, PAV1, Isolated from Pyrococcus abyssi J. Bacteriol., June 15, 2007; 189(12): 4510 - 4519. [Abstract] [Full Text] [PDF]
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S. Asgari, J. Davis, D. Wood, P. Wilson, and A. McGrath Sequence and organization of the Heliothis virescens ascovirus genome J. Gen. Virol., April 1, 2007; 88(4): 1120 - 1132. [Abstract] [Full Text] [PDF]
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H. Yukawa, C. A. Omumasaba, H. Nonaka, P. Kos, N. Okai, N. Suzuki, M. Suda, Y. Tsuge, J. Watanabe, Y. Ikeda, et al. Comparative analysis of the Corynebacterium glutamicum group and complete genome sequence of strain R Microbiology, April 1, 2007; 153(4): 1042 - 1058. [Abstract] [Full Text] [PDF]
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L. Feng, W. Wang, J. Cheng, Y. Ren, G. Zhao, C. Gao, Y. Tang, X. Liu, W. Han, X. Peng, et al. Genome and proteome of long-chain alkane degrading Geobacillus thermodenitrificans NG80-2 isolated from a deep-subsurface oil reservoir PNAS, March 27, 2007; 104(13): 5602 - 5607. [Abstract] [Full Text] [PDF]
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S. M. Faruque, V. C. Tam, N. Chowdhury, P. Diraphat, M. Dziejman, J. F. Heidelberg, J. D. Clemens, J. J. Mekalanos, and G. B. Nair Genomic analysis of the Mozambique strain of Vibrio cholerae O1 reveals the origin of El Tor strains carrying classical CTX prophage PNAS, March 20, 2007; 104(12): 5151 - 5156. [Abstract] [Full Text] [PDF]
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A. L. Delcher, K. A. Bratke, E. C. Powers, and S. L. Salzberg Identifying bacterial genes and endosymbiont DNA with Glimmer Bioinformatics, March 15, 2007; 23(6): 673 - 679. [Abstract] [Full Text] [PDF]
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A. Severin, E. Nickbarg, J. Wooters, S. A. Quazi, Y. V. Matsuka, E. Murphy, I. K. Moutsatsos, R. J. Zagursky, and S. B. Olmsted Proteomic Analysis and Identification of Streptococcus pyogenes Surface-Associated Proteins J. Bacteriol., March 1, 2007; 189(5): 1514 - 1522. [Abstract] [Full Text] [PDF]
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J. F. Challacombe, A. J. Duncan, T. S. Brettin, D. Bruce, O. Chertkov, J. C. Detter, C. S. Han, M. Misra, P. Richardson, R. Tapia, et al. Complete Genome Sequence of Haemophilus somnus (Histophilus somni) Strain 129Pt and Comparison to Haemophilus ducreyi 35000HP and Haemophilus influenzae Rd J. Bacteriol., March 1, 2007; 189(5): 1890 - 1898. [Abstract] [Full Text] [PDF]
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B. M. Fuchs, S. Spring, H. Teeling, C. Quast, J. Wulf, M. Schattenhofer, S. Yan, S. Ferriera, J. Johnson, F. O. Glockner, et al. From the Cover: Characterization of a marine gammaproteobacterium capable of aerobic anoxygenic photosynthesis PNAS, February 20, 2007; 104(8): 2891 - 2896. [Abstract] [Full Text] [PDF]
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H. Sletvold, P. J. Johnsen, G. S. Simonsen, B. Aasnaes, A. Sundsfjord, and K. M. Nielsen Comparative DNA Analysis of Two vanA Plasmids from Enterococcus faecium Strains Isolated from Poultry and a Poultry Farmer in Norway Antimicrob. Agents Chemother., February 1, 2007; 51(2): 736 - 739. [Abstract] [Full Text] [PDF]
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N. H. Bergman, K. D. Passalacqua, P. C. Hanna, and Z. S. Qin Operon Prediction for Sequenced Bacterial Genomes without Experimental Information Appl. Envir. Microbiol., February 1, 2007; 73(3): 846 - 854. [Abstract] [Full Text] [PDF]
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L. Krause, A. C. McHardy, T. W. Nattkemper, A. Puhler, J. Stoye, and F. Meyer GISMO--gene identification using a support vector machine for ORF classification Nucleic Acids Res., January 28, 2007; 35(2): 540 - 549. [Abstract] [Full Text] [PDF]
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H. Sugawara, T. Abe, T. Gojobori, and Y. Tateno DDBJ working on evaluation and classification of bacterial genes in INSDC Nucleic Acids Res., January 12, 2007; 35(suppl_1): D13 - D15. [Abstract] [Full Text] [PDF]
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E. E. Snyder, N. Kampanya, J. Lu, E. K. Nordberg, H. R. Karur, M. Shukla, J. Soneja, Y. Tian, T. Xue, H. Yoo, et al. PATRIC: The VBI PathoSystems Resource Integration Center Nucleic Acids Res., January 12, 2007; 35(suppl_1): D401 - D406. [Abstract] [Full Text] [PDF]
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F. M. McCarthy, S. M. Bridges, N. Wang, G. B. Magee, W. P. Williams, D. S. Luthe, and S. C. Burgess AgBase: a unified resource for functional analysis in agriculture Nucleic Acids Res., January 12, 2007; 35(suppl_1): D599 - D603. [Abstract] [Full Text] [PDF]
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J. A. Lanie, W.-L. Ng, K. M. Kazmierczak, T. M. Andrzejewski, T. M. Davidsen, K. J. Wayne, H. Tettelin, J. I. Glass, and M. E. Winkler Genome Sequence of Avery's Virulent Serotype 2 Strain D39 of Streptococcus pneumoniae and Comparison with That of Unencapsulated Laboratory Strain R6 J. Bacteriol., January 1, 2007; 189(1): 38 - 51. [Abstract] [Full Text] [PDF]
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A. A. Kotze, I. M. Tuffin, S. M. Deane, and D. E. Rawlings Cloning and characterization of the chromosomal arsenic resistance genes from Acidithiobacillus caldus and enhanced arsenic resistance on conjugal transfer of ars genes located on transposon TnAtcArs Microbiology, December 1, 2006; 152(12): 3551 - 3560. [Abstract] [Full Text] [PDF]
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A. Brotcke, D. S. Weiss, C. C. Kim, P. Chain, S. Malfatti, E. Garcia, and D. M. Monack Identification of MglA-Regulated Genes Reveals Novel Virulence Factors in Francisella tularensis Infect. Immun., December 1, 2006; 74(12): 6642 - 6655. [Abstract] [Full Text] [PDF]
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L. Rohmer, M. Brittnacher, K. Svensson, D. Buckley, E. Haugen, Y. Zhou, J. Chang, R. Levy, H. Hayden, M. Forsman, et al. Potential Source of Francisella tularensis Live Vaccine Strain Attenuation Determined by Genome Comparison Infect. Immun., December 1, 2006; 74(12): 6895 - 6906. [Abstract] [Full Text] [PDF]
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