Nucleic Acids Research, Vol 26, Issue 2 544-548, Copyright © 1998 by Oxford University Press
SL Salzberg, AL Delcher, S Kasif and O White
This paper describes a new system, GLIMMER, for finding genes in microbial
genomes. In a series of tests on Haemophilus influenzae , Helicobacter
pylori and other complete microbial genomes, this system has proven to be
very accurate at locating virtually all the genes in these sequences,
outperforming previous methods. A conservative estimate based on
experiments on H.pylori and H. influenzae is that the system finds >97%
of all genes. GLIMMER uses interpolated Markov models (IMMs) as a framework
for capturing dependencies between nearby nucleotides in a DNA sequence. An
IMM-based method makes predictions based on a variable context; i.e., a
variable-length oligomer in a DNA sequence. The context used by GLIMMER
changes depending on the local composition of the sequence. As a result,
GLIMMER is more flexible and more powerful than fixed-order Markov methods,
which have previously been the primary content-based technique for finding
genes in microbial DNA.
ARTICLES
Microbial gene identification using interpolated Markov models
The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA. salzberg@tigr.org
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A. T. Dobbins, M. George Jr., D. A. Basham, M. E. Ford, J. M. Houtz, M. L. Pedulla, J. G. Lawrence, G. F. Hatfull, and R. W. Hendrix Complete Genomic Sequence of the Virulent Salmonella Bacteriophage SP6 J. Bacteriol., April 1, 2004; 186(7): 1933 - 1944. [Abstract] [Full Text] [PDF]
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D. A. Rasko, J. Ravel, O. A. Okstad, E. Helgason, R. Z. Cer, L. Jiang, K. A. Shores, D. E. Fouts, N. J. Tourasse, S. V. Angiuoli, et al. The genome sequence of Bacillus cereus ATCC 10987 reveals metabolic adaptations and a large plasmid related to Bacillus anthracis pXO1 Nucleic Acids Res., February 11, 2004; 32(3): 977 - 988. [Abstract] [Full Text] [PDF]
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J. Westberg, A. Persson, A. Holmberg, A. Goesmann, J. Lundeberg, K.-E. Johansson, B. Pettersson, and M. Uhlen The Genome Sequence of Mycoplasma mycoides subsp. mycoides SC Type Strain PG1T, the Causative Agent of Contagious Bovine Pleuropneumonia (CBPP) Genome Res., February 1, 2004; 14(2): 221 - 227. [Abstract] [Full Text] [PDF]
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J. R. de la Torre, L. M. Christianson, O. Beja, M. T. Suzuki, D. M. Karl, J. Heidelberg, and E. F. DeLong Proteorhodopsin genes are distributed among divergent marine bacterial taxa PNAS, October 28, 2003; 100(22): 12830 - 12835. [Abstract] [Full Text] [PDF]
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G. Delhon, M. P. Moraes, Z. Lu, C. L. Afonso, E. F. Flores, R. Weiblen, G. F. Kutish, and D. L. Rock Genome of Bovine Herpesvirus 5 J. Virol., October 1, 2003; 77(19): 10339 - 10347. [Abstract] [Full Text] [PDF]
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K. E. Nelson, R. D. Fleischmann, R. T. DeBoy, I. T. Paulsen, D. E. Fouts, J. A. Eisen, S. C. Daugherty, R. J. Dodson, A. S. Durkin, M. Gwinn, et al. Complete Genome Sequence of the Oral Pathogenic Bacterium Porphyromonas gingivalis Strain W83 J. Bacteriol., September 15, 2003; 185(18): 5591 - 5601. [Abstract] [Full Text] [PDF]
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E. S. Miller, J. F. Heidelberg, J. A. Eisen, W. C. Nelson, A. S. Durkin, A. Ciecko, T. V. Feldblyum, O. White, I. T. Paulsen, W. C. Nierman, et al. Complete Genome Sequence of the Broad-Host-Range Vibriophage KVP40: Comparative Genomics of a T4-Related Bacteriophage J. Bacteriol., September 1, 2003; 185(17): 5220 - 5233. [Abstract] [Full Text] [PDF]
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R. Barrangou, E. Altermann, R. Hutkins, R. Cano, and T. R. Klaenhammer Functional and comparative genomic analyses of an operon involved in fructooligosaccharide utilization by Lactobacillus acidophilus PNAS, July 22, 2003; 100(15): 8957 - 8962. [Abstract] [Full Text] [PDF]
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W. H. Majoros, M. Pertea, C. Antonescu, and S. L. Salzberg GlimmerM, Exonomy and Unveil: three ab initio eukaryotic genefinders Nucleic Acids Res., July 1, 2003; 31(13): 3601 - 3604. [Abstract] [Full Text] [PDF]
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S. Bocs, S. Cruveiller, D. Vallenet, G. Nuel, and C. Medigue AMIGene: Annotation of MIcrobial Genes Nucleic Acids Res., July 1, 2003; 31(13): 3723 - 3726. [Abstract] [Full Text] [PDF]
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T. Schiex, J. Gouzy, A. Moisan, and Y. de Oliveira FrameD: a flexible program for quality check and gene prediction in prokaryotic genomes and noisy matured eukaryotic sequences Nucleic Acids Res., July 1, 2003; 31(13): 3738 - 3741. [Abstract] [Full Text] [PDF]
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M. R. Liles, B. F. Manske, S. B. Bintrim, J. Handelsman, and R. M. Goodman A Census of rRNA Genes and Linked Genomic Sequences within a Soil Metagenomic Library Appl. Envir. Microbiol., May 1, 2003; 69(5): 2684 - 2691. [Abstract] [Full Text] [PDF]
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T. D. Read, G. S. A. Myers, R. C. Brunham, W. C. Nelson, I. T. Paulsen, J. Heidelberg, E. Holtzapple, H. Khouri, N. B. Federova, H. A. Carty, et al. Genome sequence of Chlamydophila caviae (Chlamydia psittaci GPIC): examining the role of niche-specific genes in the evolution of the Chlamydiaceae Nucleic Acids Res., April 15, 2003; 31(8): 2134 - 2147. [Abstract] [Full Text] [PDF]
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F.-B. Guo, H.-Y. Ou, and C.-T. Zhang ZCURVE: a new system for recognizing protein-coding genes in bacterial and archaeal genomes Nucleic Acids Res., March 15, 2003; 31(6): 1780 - 1789. [Abstract] [Full Text] [PDF]
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E.-M. Lai, N. D. Phadke, M. T. Kachman, R. Giorno, S. Vazquez, J. A. Vazquez, J. R. Maddock, and A. Driks Proteomic Analysis of the Spore Coats of Bacillus subtilis and Bacillus anthracis J. Bacteriol., February 15, 2003; 185(4): 1443 - 1454. [Abstract] [Full Text] [PDF]
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K. Chan, S. Baker, C. C. Kim, C. S. Detweiler, G. Dougan, and S. Falkow Genomic Comparison of Salmonella enterica Serovars and Salmonella bongori by Use of an S. enterica Serovar Typhimurium DNA Microarray J. Bacteriol., January 15, 2003; 185(2): 553 - 563. [Abstract] [Full Text] [PDF]
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R. A. Welch, V. Burland, G. Plunkett III, P. Redford, P. Roesch, D. Rasko, E. L. Buckles, S.-R. Liou, A. Boutin, J. Hackett, et al. Extensive mosaic structure revealed by the complete genome sequence of uropathogenic Escherichia coli PNAS, December 24, 2002; 99(26): 17020 - 17024. [Abstract] [Full Text] [PDF]
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J. Ma, A. Campbell, and S. Karlin Correlations between Shine-Dalgarno Sequences and Gene Features Such as Predicted Expression Levels and Operon Structures J. Bacteriol., October 15, 2002; 184(20): 5733 - 5745. [Abstract] [Full Text] [PDF]
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Q. Jin, Z. Yuan, J. Xu, Y. Wang, Y. Shen, W. Lu, J. Wang, H. Liu, J. Yang, F. Yang, et al. Genome sequence of Shigella flexneri 2a: insights into pathogenicity through comparison with genomes of Escherichia coli K12 and O157 Nucleic Acids Res., October 15, 2002; 30(20): 4432 - 4441. [Abstract] [Full Text] [PDF]
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R. D. Fleischmann, D. Alland, J. A. Eisen, L. Carpenter, O. White, J. Peterson, R. DeBoy, R. Dodson, M. Gwinn, D. Haft, et al. Whole-Genome Comparison of Mycobacterium tuberculosis Clinical and Laboratory Strains J. Bacteriol., October 1, 2002; 184(19): 5479 - 5490. [Abstract] [Full Text] [PDF]
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C. Mathe, M.-F. Sagot, T. Schiex, and P. Rouze Current methods of gene prediction, their strengths and weaknesses Nucleic Acids Res., October 1, 2002; 30(19): 4103 - 4117. [Abstract] [Full Text] [PDF]
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