Bioinformatics Advance Access originally published online on January 19, 2007
Bioinformatics 2007 23(6):673-679; doi:10.1093/bioinformatics/btm009
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Identifying bacterial genes and endosymbiont DNA with Glimmer
1Center for Bioinformatics & Computational Biology, University of Maryland, College Park, MD 20742, USA
2Smurfit Institute of Genetics, University of Dublin, Trinity College Dublin, Dublin 2, Ireland
3Department of Chemical & Biomolecular Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
*To whom correspondence should be addressed.
 |
Abstract |
|---|
Motivation: The Glimmer gene-finding software has been successfully used for finding genes in bacteria, archæa and viruses representing hundreds of species. We describe several major changes to the Glimmer system, including improved methods for identifying both coding regions and start codons. We also describe a new module of Glimmer that can distinguish host and endosymbiont DNA. This module was developed in response to the discovery that eukaryotic genome sequencing projects sometimes inadvertently capture the DNA of intracellular bacteria living in the host.
Results: The new methods dramatically reduce the rate of false-positive predictions, while maintaining Glimmer's 99% sensitivity rate at detecting genes in most species, and they find substantially more correct start sites, as measured by comparisons to known and well-curated genes. We show that our interpolated Markov model (IMM) DNA discriminator correctly separated 99% of the sequences in a recent genome project that produced a mixture of sequences from the bacterium Prochloron didemni and its sea squirt host, Lissoclinum patella.
Availability: Glimmer is OSI Certified Open Source and available at http://cbcb.umd.edu/software/glimmer
Contact: adelcher{at}umiacs.umd.edu
Associate Editor: Alfonso Valencia
Received on August 3, 2006; revised on December 15, 2006; accepted on January 14, 2007
CiteULike 
Connotea 
Del.icio.us What's this?
This article has been cited by other articles:
|
|
 |
|
  P. K. Lawrence, W. Kittichotirat, R. E. Bumgarner, J. E. McDermott, D. R. Herndon, D. P. Knowles, and S. Srikumaran Genome Sequences of Mannheimia haemolytica Serotype A2: Ovine and Bovine Isolates J. Bacteriol., February 15, 2010; 192(4): 1167 - 1168. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
N. Jiao, R. Zhang, and Q. Zheng Coexistence of Two Different Photosynthetic Operons in Citromicrobium bathyomarinum JL354 As Revealed by Whole-Genome Sequencing J. Bacteriol., February 15, 2010; 192(4): 1169 - 1170. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
D. R. Herndon, G. H. Palmer, V. Shkap, D. P. Knowles Jr., and K. A. Brayton Complete Genome Sequence of Anaplasma marginale subsp. centrale J. Bacteriol., January 1, 2010; 192(1): 379 - 380. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 V. K. Sharma, N. Kumar, T. Prakash, and T. D. Taylor MetaBioME: a database to explore commercially useful enzymes in metagenomic datasets Nucleic Acids Res., January 1, 2010; 38(suppl_1): D468 - D472. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
P. S. Dehal, M. P. Joachimiak, M. N. Price, J. T. Bates, J. K. Baumohl, D. Chivian, G. D. Friedland, K. H. Huang, K. Keller, P. S. Novichkov, et al. MicrobesOnline: an integrated portal for comparative and functional genomics Nucleic Acids Res., January 1, 2010; 38(suppl_1): D396 - D400. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
C. Chen, W. Kittichotirat, Y. Si, and R. Bumgarner Genome Sequence of Aggregatibacter actinomycetemcomitans Serotype c Strain D11S-1 J. Bacteriol., December 1, 2009; 191(23): 7378 - 7379. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. Valdes, R. Quatrini, K. Hallberg, M. Dopson, P. D. T. Valenzuela, and D. S. Holmes Draft Genome Sequence of the Extremely Acidophilic Bacterium Acidithiobacillus caldus ATCC 51756 Reveals Metabolic Versatility in the Genus Acidithiobacillus J. Bacteriol., September 15, 2009; 191(18): 5877 - 5878. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
P. Romero, N. J. Croucher, N. L. Hiller, F. Z. Hu, G. D. Ehrlich, S. D. Bentley, E. Garcia, and T. J. Mitchell Comparative Genomic Analysis of Ten Streptococcus pneumoniae Temperate Bacteriophages J. Bacteriol., August 1, 2009; 191(15): 4854 - 4862. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 G.-Q. Hu, J.-T. Guo, Y.-C. Liu, and H. Zhu MetaTISA: Metagenomic Translation Initiation Site Annotator for improving gene start prediction Bioinformatics, July 15, 2009; 25(14): 1843 - 1845. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
L. Zhou, M. Pertea, A. L. Delcher, and L. Florea Sim4cc: a cross-species spliced alignment program Nucleic Acids Res., June 1, 2009; 37(11): e80 - e80. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 S. Mukhopadhyay, A. Akmal, A. C. Stewart, R.-c. Hsia, and T. D. Read Identification of Bacillus anthracis Spore Component Antigens Conserved across Diverse Bacillus cereus sensu lato Strains Mol. Cell. Proteomics, June 1, 2009; 8(6): 1174 - 1191. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 S.-F. Lan, C.-H. Huang, C.-H. Chang, W.-C. Liao, I-H. Lin, W.-N. Jian, Y.-G. Wu, S.-Y. Chen, and H.-c. Wong Characterization of a New Plasmid-Like Prophage in a Pandemic Vibrio parahaemolyticus O3:K6 Strain Appl. Envir. Microbiol., May 1, 2009; 75(9): 2659 - 2667. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
N. J. Croucher, D. Walker, P. Romero, N. Lennard, G. K. Paterson, N. C. Bason, A. M. Mitchell, M. A. Quail, P. W. Andrew, J. Parkhill, et al. Role of Conjugative Elements in the Evolution of the Multidrug-Resistant Pandemic Clone Streptococcus pneumoniaeSpain23F ST81 J. Bacteriol., March 1, 2009; 191(5): 1480 - 1489. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
S. L. Salzberg, D. Puiu, D. D. Sommer, V. Nene, and N. H. Lee Genome Sequence of the Wolbachia Endosymbiont of Culex quinquefasciatus JHB J. Bacteriol., March 1, 2009; 191(5): 1725 - 1725. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
S.-K. Lim, S. J. Kim, S. H. Cha, Y.-K. Oh, H.-J. Rhee, M.-S. Kim, and J. K. Lee Complete Genome Sequence of Rhodobacter sphaeroides KD131 J. Bacteriol., February 1, 2009; 191(3): 1118 - 1119. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 J. A. Reinhardt, D. A. Baltrus, M. T. Nishimura, W. R. Jeck, C. D. Jones, and J. L. Dangl De novo assembly using low-coverage short read sequence data from the rice pathogen Pseudomonas syringae pv. oryzae Genome Res., February 1, 2009; 19(2): 294 - 305. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. F. Kim, H. Jeong, D. S. Yu, S.-H. Choi, C.-G. Hur, M.-S. Park, S. H. Yoon, D.-W. Kim, G. E. Ji, H.-S. Park, et al. Genome Sequence of the Probiotic Bacterium Bifidobacterium animalis subsp. lactis AD011 J. Bacteriol., January 15, 2009; 191(2): 678 - 679. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
C. Winstanley, M. G.I. Langille, J. L. Fothergill, I. Kukavica-Ibrulj, C. Paradis-Bleau, F. Sanschagrin, N. R. Thomson, G. L. Winsor, M. A. Quail, N. Lennard, et al. Newly introduced genomic prophage islands are critical determinants of in vivo competitiveness in the Liverpool Epidemic Strain of Pseudomonas aeruginosa Genome Res., January 1, 2009; 19(1): 12 - 23. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
G.-Q. Hu, X. Zheng, H.-Q. Zhu, and Z.-S. She Prediction of translation initiation site for microbial genomes with TriTISA Bioinformatics, January 1, 2009; 25(1): 123 - 125. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
A. Starcevic, J. Zucko, J. Simunkovic, P. F. Long, J. Cullum, and D. Hranueli ClustScan: an integrated program package for the semi-automatic annotation of modular biosynthetic gene clusters and in silico prediction of novel chemical structures Nucleic Acids Res., December 1, 2008; 36(21): 6882 - 6892. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 H. Noguchi, T. Taniguchi, and T. Itoh MetaGeneAnnotator: Detecting Species-Specific Patterns of Ribosomal Binding Site for Precise Gene Prediction in Anonymous Prokaryotic and Phage Genomes DNA Res, December 1, 2008; 15(6): 387 - 396. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
V. Ter-Hovhannisyan, A. Lomsadze, Y. O. Chernoff, and M. Borodovsky Gene prediction in novel fungal genomes using an ab initio algorithm with unsupervised training Genome Res., December 1, 2008; 18(12): 1979 - 1990. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 Y. Chen, F. Zhou, G. Li, and Y. Xu A Recently Active Miniature Inverted-Repeat Transposable Element, Chunjie, Inserted Into an Operon Without Disturbing the Operon Structure in Geobacter uraniireducens Rf4 Genetics, August 1, 2008; 179(4): 2291 - 2297. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. Uchiyama, M. Rashel, I. Takemura, H. Wakiguchi, and S. Matsuzaki In Silico and In Vivo Evaluation of Bacteriophage {phi}EF24C, a Candidate for Treatment of Enterococcus faecalis Infections Appl. Envir. Microbiol., July 1, 2008; 74(13): 4149 - 4163. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 J. J. van Aartsen The Klebsiella pheV tRNA locus: a hotspot for integration of alien genomic islands Bioscience Horizons, March 1, 2008; 1(1): 51 - 60. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 A. Starcevic, S. Akthar, W. C. Dunlap, J. M. Shick, D. Hranueli, J. Cullum, and P. F. Long Enzymes of the shikimic acid pathway encoded in the genome of a basal metazoan, Nematostella vectensis, have microbial origins PNAS, February 19, 2008; 105(7): 2533 - 2537. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
A. Tuanyok, R. K. Auerbach, T. S. Brettin, D. C. Bruce, A. C. Munk, J. C. Detter, T. Pearson, H. Hornstra, R. W. Sermswan, V. Wuthiekanun, et al. A Horizontal Gene Transfer Event Defines Two Distinct Groups within Burkholderia pseudomallei That Have Dissimilar Geographic Distributions J. Bacteriol., December 15, 2007; 189(24): 9044 - 9049. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. P. McCutcheon and N. A. Moran Parallel genomic evolution and metabolic interdependence in an ancient symbiosis PNAS, December 4, 2007; 104(49): 19392 - 19397. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
N. J. Hillson, P. Hu, G. L. Andersen, and L. Shapiro Caulobacter crescentus as a Whole-Cell Uranium Biosensor Appl. Envir. Microbiol., December 1, 2007; 73(23): 7615 - 7621. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
D. Sulakhe, M. D'Souza, M. Syed, A. Rodriguez, Y. Zhang, E. M. Glass, M. F. Romine, and N. Maltsev GNARE--a grid-based server for the analysis of user submitted genomes Nucleic Acids Res., May 25, 2007; (2007) gkm366v1. [Abstract] [Full Text] [PDF]
|
|