Bioinformatics Vol. 16 no. 6 2000
Pages 560-561
© 2000 Oxford University Press
Applications Note |
Oriloc: prediction of replication boundaries in unannotated bacterial chromosomes
1 Laboratoire BBE-CNRS UMR 5558, UniversitéClaude Bernard, 43 Bd. du 11 Novembre 1918, F-69622 Villeurbanne cedex, France
Received on November 26, 1999
; accepted on January 21, 2000
Summary: A program called Oriloc has been developed for the prediction of bacterial replication origins. The method builds on the fact that there are compositional asymmetries between the leading and the lagging strand for replication. The program works with unannotated sequences in fasta format and therefore uses glimmer 2.0 outputs to discriminate between codon positions so as to increase the signal/noise ratio.
Availability: The ANSI C source code is freely available for academic use at ftp://pbil.univ-lyon1.fr/pub/logiciel/oriloc/oriloc.c.
Contact: lobry{at}biomserv.univ-lyon1.fr
Supplementary information: ftp://pbil.univ-lyon1.fr/pub/logiciel/oriloc/oriloc.ps
* To whom correspondence should be addressed.
CiteULike 
Connotea 
Del.icio.us What's this?
This article has been cited by other articles:
|
|
 |
|
  B.R. Powdel, S. S. Satapathy, A. Kumar, P. K. Jha, A. K. Buragohain, M. Borah, and S. K. Ray A Study in Entire Chromosomes of Violations of the Intra-strand Parity of Complementary Nucleotides (Chargaff's Second Parity Rule) DNA Res, December 1, 2009; 16(6): 325 - 343. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 R. Barrangou, E. P. Briczinski, L. L. Traeger, J. R. Loquasto, M. Richards, P. Horvath, A.-C. Coute-Monvoisin, G. Leyer, S. Rendulic, J. L. Steele, et al. Comparison of the Complete Genome Sequences of Bifidobacterium animalis subsp. lactis DSM 10140 and Bl-04 J. Bacteriol., July 1, 2009; 191(13): 4144 - 4151. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 E. V. Koonin and Y. I. Wolf Genomics of bacteria and archaea: the emerging dynamic view of the prokaryotic world Nucleic Acids Res., December 1, 2008; 36(21): 6688 - 6719. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 N. V. Sernova and M. S. Gelfand Identification of replication origins in prokaryotic genomes Brief Bioinform, September 1, 2008; 9(5): 376 - 391. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 A. Necsulea and J. R. Lobry A New Method for Assessing the Effect of Replication on DNA Base Composition Asymmetry Mol. Biol. Evol., October 1, 2007; 24(10): 2169 - 2179. [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]
|
|
|
|
|
|
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]
|
|
|
|
|
|
C. Nikolaou and Y. Almirantis A study on the correlation of nucleotide skews and the positioning of the origin of replication: different modes of replication in bacterial species Nucleic Acids Res., November 30, 2005; 33(21): 6816 - 6822. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
P. Mackiewicz, J. Zakrzewska-Czerwinska, A. Zawilak, M. R. Dudek, and S. Cebrat Where does bacterial replication start? Rules for predicting the oriC region Nucleic Acids Res., July 16, 2004; 32(13): 3781 - 3791. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
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]
|
|
|
|
 |
|
 R. Gil, F. J. Silva, E. Zientz, F. Delmotte, F. Gonzalez-Candelas, A. Latorre, C. Rausell, J. Kamerbeek, J. Gadau, B. Holldobler, et al. The genome sequence of Blochmannia floridanus: Comparative analysis of reduced genomes PNAS, August 5, 2003; 100(16): 9388 - 9393. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
V. Daubin and G. Perriere G+C3 Structuring Along the Genome: A Common Feature in Prokaryotes Mol. Biol. Evol., April 1, 2003; 20(4): 471 - 483. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
M. A. Schell, M. Karmirantzou, B. Snel, D. Vilanova, B. Berger, G. Pessi, M.-C. Zwahlen, F. Desiere, P. Bork, M. Delley, et al. The genome sequence of Bifidobacterium longum reflects its adaptation to the human gastrointestinal tract PNAS, October 29, 2002; 99(22): 14422 - 14427. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
S. Guindon and G. Perriere Intragenomic Base Content Variation Is a Potential Source of Biases When Searching for Horizontally Transferred Genes Mol. Biol. Evol., September 1, 2001; 18(9): 1838 - 1840. [Full Text] [PDF]
|
|