Ori-Finder: A web-based system for finding oriCs in unannotated bacterial genomes

BMC Bioinformatics

Volumn 9, Issue , 2008, Pages

  Gao, Feng ^a   Zhang, Chun Ting ^a  

^a TIANJIN UNIVERSITY   (China)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL CELL CYCLE; BACTERIAL GENOMES; CHROMOSOMAL REPLICATION; GENOME SEQUENCES; GENOME SEQUENCING; INTEGRATED METHOD; REPLICATION ORIGIN; WEB-BASED SYSTEM;

GENETIC ENGINEERING; WORLD WIDE WEB;

GENES;

REPLICATION INITIATOR PROTEIN DNAA;

ARTICLE; BACTERIAL GENOME; CHROMOSOME REPLICATION; COMPUTER GRAPHICS; COMPUTER PROGRAM; DNA BASE COMPOSITION; DNA REPLICATION ORIGIN; GENE IDENTIFICATION; GENE SEQUENCE; GENETIC ANALYSIS; MOLECULAR PHYLOGENY; NONHUMAN; NUCLEOTIDE SEQUENCE; ONLINE SYSTEM; PREDICTION; SEQUENCE ANALYSIS; ALGORITHM; CHROMOSOME MAP; COMPUTER INTERFACE; DNA SEQUENCE; GENETICS; INFORMATION RETRIEVAL; INFORMATION SYSTEM; INTERNET; METHODOLOGY; MOLECULAR GENETICS;

ARCHAEA; BACTERIA (MICROORGANISMS);

ALGORITHMS; BASE SEQUENCE; CHROMOSOME MAPPING; GENOME, BACTERIAL; INFORMATION STORAGE AND RETRIEVAL; INFORMATION SYSTEMS; INTERNET; MOLECULAR SEQUENCE DATA; REPLICATION ORIGIN; SEQUENCE ANALYSIS, DNA; SOFTWARE; USER-COMPUTER INTERFACE;

EID: 41349112730     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-9-79     Document Type: Article

References (15)

1. Robinson NP Bell SD Origins of DNA replication in the three domains of life The FEBS journal 2005, 272(15):3757-3766. 10.1111/ j.1742-4658.2005.04768.x 16045748
2. Necsulea A Lobry JR A new method for assessing the effect of replication on DNA base composition asymmetry Molecular biology and evolution 2007, 24(10):2169-2179. 10.1093/molbev/msm148
3. Lobry JR A simple vectorial representation of DNA sequences for the detection of replication origins in bacteria Biochimie 1996, 78(5):323-326. 10.1016/0300-9084(96)84764-X 8905151
4. Grigoriev A Analyzing genomes with cumulative skew diagrams Nucleic acids research 1998, 26(10):2286-2290. 147580 9580676 10.1093/nar/ 26.10.2286
5. Frank AC Lobry JR Oriloc: Prediction of replication boundaries in unannotated bacterial chromosomes Bioinformatics 2000, 16(6):560-561. 10.1093/bioinformatics/16.6.560 10980154
6. Salzberg SL Salzberg AJ Kerlavage AR Tomb JF Skewed oligomers and origins of replication Gene 1998, 217(1-2):57-67. 10.1016/ S0378-1119(98)00374-6 9795135
7. Worning P Jensen LJ Hallin PF Staerfeldt HH Ussery DW Origin of replication in circular prokaryotic chromosomes Environmental microbiology 2006, 8(2):353-361. 10.1111/j.1462-2920.2005.00917.x 16423021
8. Mackiewicz P Zakrzewska-Czerwinska J Zawilak A Dudek MR Cebrat S Where does bacterial replication start? Rules for predicting the oriC region Nucleic acids research 2004, 32(13):3781-3791. 506792 15258248 10.1093/ nar/gkh699
9. Gnuplot homepage http://www.gnuplot.info
10. Zhang R Zhang CT Identification of replication origins in archaeal genomes based on the Z-curve method Archaea 2005, 1(5):335-346. 15876567
11. Guo FB Ou HY Zhang CT ZCURVE: A new system for recognizing protein-coding genes in bacterial and archaeal genomes Nucleic acids research 2003, 31(6):1780-1789. 152858 12626720 10.1093/nar/gkg254
12. NCBI's RefSeq ftp site ftp://ftp.ncbi.nih.gov/genomes
13. Gao F Zhang CT DoriC: A database of oriC regions in bacterial genomes Bioinformatics 2007, 23(14):1866-1867. 10.1093/bioinformatics/btm255 17496319
14. Allewalt JP Bateson MM Revsbech NP Slack K Ward DM Effect of temperature and light on growth of and photosynthesis by Synechococcus isolates typical of those predominating in the octopus spring microbial mat community of Yellowstone National Park Applied and environmental microbiology 2006, 72(1):544-550. 10.1128/AEM.72.1.544-550.2006
15. DoriC http://tubic.tju.edu.cn/doric