Molecular Biology and Evolution, Vol 16, 512-524, Copyright © 1999 by Society for Molecular Biology and Evolution
JH Badger and GJ Olsen
Gene recognition is essential to understanding existing and future DNA
sequence data. CRITICA (Coding Region Identification Tool Invoking
Comparative Analysis) is a suite of programs for identifying likely
protein-coding sequences in DNA by combining comparative analysis of DNA
sequences with more common noncomparative methods. In the comparative
component of the analysis, regions of DNA are aligned with related
sequences from the DNA databases; if the translation of the aligned
sequences has greater amino acid identity than expected for the observed
percentage nucleotide identity, this is interpreted as evidence for coding.
CRITICA also incorporates noncomparative information derived from the
relative frequencies of hexanucleotides in coding frames versus other
contexts (i.e., dicodon bias). The dicodon usage information is derived by
iterative analysis of the data, such that CRITICA is not dependent on the
existence or accuracy of coding sequence annotations in the databases. This
independence makes the method particularly well suited for the analysis of
novel genomes. CRITICA was tested by analyzing the available Salmonella
typhimurium DNA sequences. Its predictions were compared with the DNA
sequence annotations and with the predictions of GenMark. CRITICA proved to
be more accurate than GenMark, and moreover, many of its predictions that
would seem to be errors instead reflect problems in the sequence databases.
The source code of CRITICA is freely available by anonymous FTP
(rdp.life.uiuc.edu in/pub/critica) and on the World Wide Web
(http:/(/)rdpwww.life.uiuc.edu).
ORIGINAL ARTICLE
CRITICA: coding region identification tool invoking comparative analysis
Department of Microbiology, University of Illinois, Urbana 61801, USA.
CiteULike 
Connotea 
Del.icio.us What's this?
This article has been cited by other articles:
|
|
 |
|
  U. Wegmann, K. Overweg, N. Horn, A. Goesmann, A. Narbad, M. J. Gasson, and C. Shearman Complete Genome Sequence of Lactobacillus johnsonii FI9785, a Competitive Exclusion Agent against Pathogens in Poultry J. Bacteriol., November 15, 2009; 191(22): 7142 - 7143. [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., November 11, 2009; (2009) gkp919v1. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 P. P. Amaral, C. Neyt, S. J. Wilkins, M. E. Askarian-Amiri, S. M. Sunkin, A. C. Perkins, and J. S. Mattick Complex architecture and regulated expression of the Sox2ot locus during vertebrate development RNA, November 1, 2009; 15(11): 2013 - 2027. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. Zhang and G. J. Olsen Messenger RNA processing in Methanocaldococcus (Methanococcus) jannaschii RNA, October 1, 2009; 15(10): 1909 - 1916. [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]
|
|
|
|
 |
|
 G. Solda, I. V. Makunin, O. U. Sezerman, A. Corradin, G. Corti, and A. Guffanti An Ariadne's thread to the identification and annotation of noncoding RNAs in eukaryotes Brief Bioinform, September 1, 2009; 10(5): 475 - 489. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 S. Schubbe, T. J. Williams, G. Xie, H. E. Kiss, T. S. Brettin, D. Martinez, C. A. Ross, D. Schuler, B. L. Cox, K. H. Nealson, et al. Complete Genome Sequence of the Chemolithoautotrophic Marine Magnetotactic Coccus Strain MC-1 Appl. Envir. Microbiol., July 15, 2009; 75(14): 4835 - 4852. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
D. S. A. Goltsman, V. J. Denef, S. W. Singer, N. C. VerBerkmoes, M. Lefsrud, R. S. Mueller, G. J. Dick, C. L. Sun, K. E. Wheeler, A. Zemla, et al. Community Genomic and Proteomic Analyses of Chemoautotrophic Iron-Oxidizing "Leptospirillum rubarum" (Group II) and "Leptospirillum ferrodiazotrophum" (Group III) Bacteria in Acid Mine Drainage Biofilms Appl. Envir. Microbiol., July 1, 2009; 75(13): 4599 - 4615. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 M. Hiller, S. Findeiss, S. Lein, M. Marz, C. Nickel, D. Rose, C. Schulz, R. Backofen, S. J. Prohaska, G. Reuter, et al. Conserved introns reveal novel transcripts in Drosophila melanogaster Genome Res., July 1, 2009; 19(7): 1289 - 1300. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 K. C. Pang, M. E. Dinger, T. R. Mercer, L. Malquori, S. M. Grimmond, W. Chen, and J. S. Mattick Genome-Wide Identification of Long Noncoding RNAs in CD8+ T Cells J. Immunol., June 15, 2009; 182(12): 7738 - 7748. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. Zhang, E. Li, and G. J. Olsen Protein-coding gene promoters in Methanocaldococcus (Methanococcus) jannaschii Nucleic Acids Res., June 1, 2009; 37(11): 3588 - 3601. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 L. Klasson, J. Westberg, P. Sapountzis, K. Naslund, Y. Lutnaes, A. C. Darby, Z. Veneti, L. Chen, H. R. Braig, R. Garrett, et al. The mosaic genome structure of the Wolbachia wRi strain infecting Drosophila simulans PNAS, April 7, 2009; 106(14): 5725 - 5730. [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]
|
|
|
|
 |
|
 V. Kunin, A. Copeland, A. Lapidus, K. Mavromatis, and P. Hugenholtz A Bioinformatician's Guide to Metagenomics Microbiol. Mol. Biol. Rev., December 1, 2008; 72(4): 557 - 578. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
E. Li, C. I. Reich, and G. J. Olsen A whole-genome approach to identifying protein binding sites: promoters in Methanocaldococcus (Methanococcus) jannaschii Nucleic Acids Res., December 1, 2008; 36(22): 6948 - 6958. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
H. J. G. van de Werken, M. R. A. Verhaart, A. L. VanFossen, K. Willquist, D. L. Lewis, J. D. Nichols, H. P. Goorissen, E. F. Mongodin, K. E. Nelson, E. W. J. van Niel, et al. Hydrogenomics of the Extremely Thermophilic Bacterium Caldicellulosiruptor saccharolyticus Appl. Envir. Microbiol., November 1, 2008; 74(21): 6720 - 6729. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
T. E. Mattes, A. K. Alexander, P. M. Richardson, A. C. Munk, C. S. Han, P. Stothard, and N. V. Coleman The Genome of Polaromonas sp. Strain JS666: Insights into the Evolution of a Hydrocarbon- and Xenobiotic-Degrading Bacterium, and Features of Relevance to Biotechnology Appl. Envir. Microbiol., October 15, 2008; 74(20): 6405 - 6416. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
E. A. Welsh, M. Liberton, J. Stockel, T. Loh, T. Elvitigala, C. Wang, A. Wollam, R. S. Fulton, S. W. Clifton, J. M. Jacobs, et al. The genome of Cyanothece 51142, a unicellular diazotrophic cyanobacterium important in the marine nitrogen cycle PNAS, September 30, 2008; 105(39): 15094 - 15099. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 M. Naito, H. Hirakawa, A. Yamashita, N. Ohara, M. Shoji, H. Yukitake, K. Nakayama, H. Toh, F. Yoshimura, S. Kuhara, et al. Determination of the Genome Sequence of Porphyromonas gingivalis Strain ATCC 33277 and Genomic Comparison with Strain W83 Revealed Extensive Genome Rearrangements in P. gingivalis DNA Res, August 1, 2008; 15(4): 215 - 225. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
I. Anderson, J. Rodriguez, D. Susanti, I. Porat, C. Reich, L. E. Ulrich, J. G. Elkins, K. Mavromatis, A. Lykidis, E. Kim, et al. Genome Sequence of Thermofilum pendens Reveals an Exceptional Loss of Biosynthetic Pathways without Genome Reduction J. Bacteriol., April 15, 2008; 190(8): 2957 - 2965. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 C. Ansong, S. O. Purvine, J. N. Adkins, M. S. Lipton, and R. D. Smith Proteogenomics: needs and roles to be filled by proteomics in genome annotation Brief Funct Genomic Proteomic, March 10, 2008; (2008) eln010v1. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
T. Kosaka, S. Kato, T. Shimoyama, S. Ishii, T. Abe, and K. Watanabe The genome of Pelotomaculum thermopropionicum reveals niche-associated evolution in anaerobic microbiota Genome Res., March 1, 2008; 18(3): 442 - 448. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
T. Goto, A. Yamashita, H. Hirakawa, M. Matsutani, K. Todo, K. Ohshima, H. Toh, K. Miyamoto, S. Kuhara, M. Hattori, et al. Complete Genome Sequence of Finegoldia magna, an Anaerobic Opportunistic Pathogen DNA Res, February 7, 2008; (2008) dsm030v1. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
T. Mourier, C. Carret, S. Kyes, Z. Christodoulou, P. P. Gardner, D. C. Jeffares, R. Pinches, B. Barrell, M. Berriman, S. Griffiths-Jones, et al. Genome-wide discovery and verification of novel structured RNAs in Plasmodium falciparum Genome Res., February 1, 2008; 18(2): 281 - 292. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
T. R. Mercer, M. E. Dinger, S. M. Sunkin, M. F. Mehler, and J. S. Mattick Specific expression of long noncoding RNAs in the mouse brain PNAS, January 15, 2008; 105(2): 716 - 721. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 C. Meisinger-Henschel, M. Schmidt, S. Lukassen, B. Linke, L. Krause, S. Konietzny, A. Goesmann, P. Howley, P. Chaplin, M. Suter, et al. Genomic sequence of chorioallantois vaccinia virus Ankara, the ancestor of modified vaccinia virus Ankara J. Gen. Virol., December 1, 2007; 88(12): 3249 - 3259. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
O. I. Rzhepishevska, J. Valdes, L. Marcinkeviciene, C. A. Gallardo, R. Meskys, V. Bonnefoy, D. S. Holmes, and M. Dopson Regulation of a Novel Acidithiobacillus caldus Gene Cluster Involved in Metabolism of Reduced Inorganic Sulfur Compounds Appl. Envir. Microbiol., November 15, 2007; 73(22): 7367 - 7372. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 S. Kang, S.-J. Yang, S. Kim, and J. Bhak CONSORF: a consensus prediction system for prokaryotic coding sequences Bioinformatics, November 15, 2007; 23(22): 3088 - 3090. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
M. Richter, M. Kube, D. A. Bazylinski, T. Lombardot, F. O. Glockner, R. Reinhardt, and D. Schuler Comparative Genome Analysis of Four Magnetotactic Bacteria Reveals a Complex Set of Group-Specific Genes Implicated in Magnetosome Biomineralization and Function J. Bacteriol., July 1, 2007; 189(13): 4899 - 4910. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
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]
|
|
|
|
|
|
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]
|
|
|
|
|
|
N.-H. Cho, H.-R. Kim, J.-H. Lee, S.-Y. Kim, J. Kim, S. Cha, S.-Y. Kim, A. C. Darby, H.-H. Fuxelius, J. Yin, et al. The Orientia tsutsugamushi genome reveals massive proliferation of conjugative type IV secretion system and host cell interaction genes PNAS, May 8, 2007; 104(19): 7981 - 7986. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. Ponjavic, C. P. Ponting, and G. Lunter Functionality or transcriptional noise? Evidence for selection within long noncoding RNAs Genome Res., May 1, 2007; 17(5): 556 - 565. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
U. Wegmann, M. O'Connell-Motherway, A. Zomer, G. Buist, C. Shearman, C. Canchaya, M. Ventura, A. Goesmann, M. J. Gasson, O. P. Kuipers, et al. Complete Genome Sequence of the Prototype Lactic Acid Bacterium Lactococcus lactis subsp. cremoris MG1363 J. Bacteriol., April 15, 2007; 189(8): 3256 - 3270. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
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]
|
|
|
|
|
|
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]
|
|
|
|
|
|
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]
|
|
|
|
|
|
D. L. Maeder, I. Anderson, T. S. Brettin, D. C. Bruce, P. Gilna, C. S. Han, A. Lapidus, W. W. Metcalf, E. Saunders, R. Tapia, et al. The Methanosarcina barkeri Genome: Comparative Analysis with Methanosarcina acetivorans and Methanosarcina mazei Reveals Extensive Rearrangement within Methanosarcinal Genomes J. Bacteriol., November 15, 2006; 188(22): 7922 - 7931. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
P. S. G. Chain, V. J. Denef, K. T. Konstantinidis, L. M. Vergez, L. Agullo, V. L. Reyes, L. Hauser, M. Cordova, L. Gomez, M. Gonzalez, et al. Inaugural Article: Burkholderia xenovorans LB400 harbors a multi-replicon, 9.73-Mbp genome shaped for versatility PNAS, October 17, 2006; 103(42): 15280 - 15287. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
X. Bai, J. Zhang, A. Ewing, S. A. Miller, A. Jancso Radek, D. V. Shevchenko, K. Tsukerman, T. Walunas, A. Lapidus, J. W. Campbell, et al. Living with genome instability: the adaptation of phytoplasmas to diverse environments of their insect and plant hosts. J. Bacteriol., May 1, 2006; 188(10): 3682 - 3696. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 M. Liu, M. D. Healy, B. A. Dougherty, K. M. Esposito, T. C. Maurice, C. E. Mazzucco, R. E. Bruccoleri, D. B. Davison, M. Frosco, J. F. Barrett, et al. Conserved fungal genes as potential targets for broad-spectrum antifungal drug discovery. Eukaryot. Cell, April 1, 2006; 5(4): 638 - 649. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
T. Ravasi, H. Suzuki, K. C. Pang, S. Katayama, M. Furuno, R. Okunishi, S. Fukuda, K. Ru, M. C. Frith, M. M. Gongora, et al. Experimental validation of the regulated expression of large numbers of non-coding RNAs from the mouse genome Genome Res., January 1, 2006; 16(1): 11 - 19. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
H. Jeong, J. H. Yim, C. Lee, S.-H. Choi, Y. K. Park, S. H. Yoon, C.-G. Hur, H.-Y. Kang, D. Kim, H. H. Lee, et al. Genomic blueprint of Hahella chejuensis, a marine microbe producing an algicidal agent Nucleic Acids Res., December 13, 2005; 33(22): 7066 - 7073. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
F. Thieme, R. Koebnik, T. Bekel, C. Berger, J. Boch, D. Buttner, C. Caldana, L. Gaigalat, A. Goesmann, S. Kay, et al. Insights into Genome Plasticity and Pathogenicity of the Plant Pathogenic Bacterium Xanthomonas campestris pv. vesicatoria Revealed by the Complete Genome Sequence J. Bacteriol., November 1, 2005; 187(21): 7254 - 7266. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
M. Falb, F. Pfeiffer, P. Palm, K. Rodewald, V. Hickmann, J. Tittor, and D. Oesterhelt Living with two extremes: Conclusions from the genome sequence of Natronomonas pharaonis Genome Res., October 1, 2005; 15(10): 1336 - 1343. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
E. J. Alm, K. H. Huang, M. N. Price, R. P. Koche, K. Keller, I. L. Dubchak, and A. P. Arkin The MicrobesOnline Web site for comparative genomics Genome Res., July 1, 2005; 15(7): 1015 - 1022. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
A. Goesmann, B. Linke, D. Bartels, M. Dondrup, L. Krause, H. Neuweger, S. Oehm, T. Paczian, A. Wilke, and F. Meyer BRIGEP--the BRIDGE-based genome-transcriptome-proteome browser Nucleic Acids Res., July 1, 2005; 33(suppl_2): W710 - W716. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
M. A. Patrauchan, C. Florizone, M. Dosanjh, W. W. Mohn, J. Davies, and L. D. Eltis Catabolism of Benzoate and Phthalate in Rhodococcus sp. Strain RHA1: Redundancies and Convergence J. Bacteriol., June 15, 2005; 187(12): 4050 - 4063. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
T. Fukui, H. Atomi, T. Kanai, R. Matsumi, S. Fujiwara, and T. Imanaka Complete genome sequence of the hyperthermophilic archaeon Thermococcus kodakaraensis KOD1 and comparison with Pyrococcus genomes Genome Res., March 1, 2005; 15(3): 352 - 363. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
M. N. Price, K. H. Huang, E. J. Alm, and A. P. Arkin A novel method for accurate operon predictions in all sequenced prokaryotes Nucleic Acids Res., February 8, 2005; 33(3): 880 - 892. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
X.-F. Wan, N. C. VerBerkmoes, L. A. McCue, D. Stanek, H. Connelly, L. J. Hauser, L. Wu, X. Liu, T. Yan, A. Leaphart, et al. Transcriptomic and Proteomic Characterization of the Fur Modulon in the Metal-Reducing Bacterium Shewanella oneidensis J. Bacteriol., December 15, 2004; 186(24): 8385 - 8400. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
Z. I. Johnson and S. W. Chisholm Properties of overlapping genes are conserved across microbial genomes Genome Res., November 1, 2004; 14(11): 2268 - 2272. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
T. Kuwahara, A. Yamashita, H. Hirakawa, H. Nakayama, H. Toh, N. Okada, S. Kuhara, M. Hattori, T. Hayashi, and Y. Ohnishi Genomic analysis of Bacteroides fragilis reveals extensive DNA inversions regulating cell surface adaptation PNAS, October 12, 2004; 101(41): 14919 - 14924. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
A. Bolotin, B. Quinquis, A. Sorokin, and D. S. Ehrlich Recent Genetic Transfer between Lactococcus lactis and Enterobacteria J. Bacteriol., October 1, 2004; 186(19): 6671 - 6677. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
A. A. Best, H. G. Morrison, A. G. McArthur, M. L. Sogin, and G. J. Olsen Evolution of Eukaryotic Transcription: Insights From the Genome of Giardia lamblia Genome Res., August 1, 2004; 14(8): 1537 - 1547. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
O. Futterer, A. Angelov, H. Liesegang, G. Gottschalk, C. Schleper, B. Schepers, C. Dock, G. Antranikian, and W. Liebl Genome sequence of Picrophilus torridus and its implications for life around pH 0 PNAS, June 15, 2004; 101(24): 9091 - 9096. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
A. Dufresne, M. Salanoubat, F. Partensky, F. Artiguenave, I. M. Axmann, V. Barbe, S. Duprat, M. Y. Galperin, E. V. Koonin, F. Le Gall, et al. From the Cover: Genome sequence of the cyanobacterium Prochlorococcus marinus SS120, a nearly minimal oxyphototrophic genome PNAS, August 19, 2003; 100(17): 10020 - 10025. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
F. Mignone, G. Grillo, S. Liuni, and G. Pesole Computational identification of protein coding potential of conserved sequence tags through cross-species evolutionary analysis Nucleic Acids Res., August 1, 2003; 31(15): 4639 - 4645. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
F. O. Glockner, M. Kube, M. Bauer, H. Teeling, T. Lombardot, W. Ludwig, D. Gade, A. Beck, K. Borzym, K. Heitmann, et al. Complete genome sequence of the marine planctomycete Pirellula sp. strain 1 PNAS, July 8, 2003; 100(14): 8298 - 8303. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
N. F.W. Saunders, T. Thomas, P. M.G. Curmi, J. S. Mattick, E. Kuczek, R. Slade, J. Davis, P. D. Franzmann, D. Boone, K. Rusterholtz, et al. Mechanisms of Thermal Adaptation Revealed From the Genomes of the Antarctic Archaea Methanogenium frigidum and Methanococcoides burtonii Genome Res., July 1, 2003; 13(7): 1580 - 1588. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 M. W. Hahn, J. E. Stajich, and G. A. Wray The Effects of Selection Against Spurious Transcription Factor Binding Sites Mol. Biol. Evol., June 1, 2003; 20(6): 901 - 906. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
P. Chain, J. Lamerdin, F. Larimer, W. Regala, V. Lao, M. Land, L. Hauser, A. Hooper, M. Klotz, J. Norton, et al. Complete Genome Sequence of the Ammonia-Oxidizing Bacterium and Obligate Chemolithoautotroph Nitrosomonas europaea J. Bacteriol., May 1, 2003; 185(9): 2759 - 2773. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
F. Meyer, A. Goesmann, A. C. McHardy, D. Bartels, T. Bekel, J. Clausen, J. Kalinowski, B. Linke, O. Rupp, R. Giegerich, et al. GenDB--an open source genome annotation system for prokaryote genomes Nucleic Acids Res., April 15, 2003; 31(8): 2187 - 2195. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
T. Shibuya and I. Rigoutsos Dictionary-driven prokaryotic gene finding Nucleic Acids Res., June 15, 2002; 30(12): 2710 - 2725. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
E. Selkov, R. Overbeek, Y. Kogan, L. Chu, V. Vonstein, D. Holmes, S. Silver, R. Haselkorn, and M. Fonstein Functional analysis of gapped microbial genomes: Amino acid metabolism of Thiobacillus ferrooxidans PNAS, March 28, 2000; 97(7): 3509 - 3514. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
R. Overbeek, N. Larsen, G. D. Pusch, M. D'Souza, E. S. Jr, N. Kyrpides, M. Fonstein, N. Maltsev, and E. Selkov WIT: integrated system for high-throughput genome sequence analysis and metabolic reconstruction Nucleic Acids Res., January 1, 2000; 28(1): 123 - 125. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
D. E. Graham, R. Overbeek, G. J. Olsen, and C. R. Woese An archaeal genomic signature PNAS, March 28, 2000; 97(7): 3304 - 3308. [Abstract] [Full Text] [PDF]
|
|