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

BACKGROUND: Chromosomal replication is the central event in the bacterial cell cycle. Identification of replication origins (oriCs) is necessary for almost all newly sequenced bacterial genomes. Given the increasing pace of genome sequencing, the current available software for predicting oriCs, howe...

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Detalles Bibliográficos
Autores principales: Gao, Feng, Zhang, Chun-Ting
Formato: Texto
Lenguaje:English
Publicado: BioMed Central 2008
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2275245/
https://www.ncbi.nlm.nih.gov/pubmed/18237442
http://dx.doi.org/10.1186/1471-2105-9-79
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author Gao, Feng
Zhang, Chun-Ting
author_facet Gao, Feng
Zhang, Chun-Ting
author_sort Gao, Feng
collection PubMed
description BACKGROUND: Chromosomal replication is the central event in the bacterial cell cycle. Identification of replication origins (oriCs) is necessary for almost all newly sequenced bacterial genomes. Given the increasing pace of genome sequencing, the current available software for predicting oriCs, however, still leaves much to be desired. Therefore, the increasing availability of genome sequences calls for improved software to identify oriCs in newly sequenced and unannotated bacterial genomes. RESULTS: We have developed Ori-Finder, an online system for finding oriCs in bacterial genomes based on an integrated method comprising the analysis of base composition asymmetry using the Z-curve method, distribution of DnaA boxes, and the occurrence of genes frequently close to oriCs. The program can also deal with unannotated genome sequences by integrating the gene-finding program ZCURVE 1.02. Output of the predicted results is exported to an HTML report, which offers convenient views on the results in both graphical and tabular formats. CONCLUSION: A web-based system to predict replication origins of bacterial genomes has been presented here. Based on this system, oriC regions have been predicted for the bacterial genomes available in GenBank currently. It is hoped that Ori-Finder will become a useful tool for the identification and analysis of oriCs in both bacterial and archaeal genomes.
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spelling pubmed-22752452008-03-26 Ori-Finder: A web-based system for finding oriCs in unannotated bacterial genomes Gao, Feng Zhang, Chun-Ting BMC Bioinformatics Software BACKGROUND: Chromosomal replication is the central event in the bacterial cell cycle. Identification of replication origins (oriCs) is necessary for almost all newly sequenced bacterial genomes. Given the increasing pace of genome sequencing, the current available software for predicting oriCs, however, still leaves much to be desired. Therefore, the increasing availability of genome sequences calls for improved software to identify oriCs in newly sequenced and unannotated bacterial genomes. RESULTS: We have developed Ori-Finder, an online system for finding oriCs in bacterial genomes based on an integrated method comprising the analysis of base composition asymmetry using the Z-curve method, distribution of DnaA boxes, and the occurrence of genes frequently close to oriCs. The program can also deal with unannotated genome sequences by integrating the gene-finding program ZCURVE 1.02. Output of the predicted results is exported to an HTML report, which offers convenient views on the results in both graphical and tabular formats. CONCLUSION: A web-based system to predict replication origins of bacterial genomes has been presented here. Based on this system, oriC regions have been predicted for the bacterial genomes available in GenBank currently. It is hoped that Ori-Finder will become a useful tool for the identification and analysis of oriCs in both bacterial and archaeal genomes. BioMed Central 2008-02-01 /pmc/articles/PMC2275245/ /pubmed/18237442 http://dx.doi.org/10.1186/1471-2105-9-79 Text en Copyright © 2008 Gao and Zhang; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( (http://creativecommons.org/licenses/by/2.0) ), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Software
Gao, Feng
Zhang, Chun-Ting
Ori-Finder: A web-based system for finding oriCs in unannotated bacterial genomes
title Ori-Finder: A web-based system for finding oriCs in unannotated bacterial genomes
title_full Ori-Finder: A web-based system for finding oriCs in unannotated bacterial genomes
title_fullStr Ori-Finder: A web-based system for finding oriCs in unannotated bacterial genomes
title_full_unstemmed Ori-Finder: A web-based system for finding oriCs in unannotated bacterial genomes
title_short Ori-Finder: A web-based system for finding oriCs in unannotated bacterial genomes
title_sort ori-finder: a web-based system for finding orics in unannotated bacterial genomes
topic Software
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2275245/
https://www.ncbi.nlm.nih.gov/pubmed/18237442
http://dx.doi.org/10.1186/1471-2105-9-79
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