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Nucleic Acids Research 2005 33(Web Server Issue):W734-W740; doi:10.1093/nar/gki361
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© The Author 2005. Published by Oxford University Press. All rights reserved
The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use, please contact journals.permissions{at}oupjournals.org

Article

The bioinformatics resource for oral pathogens

Tsute Chen*, Kevin Abbey, Wen-jie Deng and Meng-chuan Cheng

The Forsyth Institute 140 Fenway, Boston, MA 02115, USA

*To whom correspondence should be addressed. Tel: +1 617 892 8359; Fax: +1 617 262 5200; Email: tchen{at}forsyth.org

Received January 21, 2005. Revised February 22, 2005. Accepted February 22, 2005.

Complete genomic sequences of several oral pathogens have been deciphered and multiple sources of independently annotated data are available for the same genomes. Different gene identification schemes and functional annotation methods used in these databases present a challenge for cross-referencing and the efficient use of the data. The Bioinformatics Resource for Oral Pathogens (BROP) aims to integrate bioinformatics data from multiple sources for easy comparison, analysis and data-mining through specially designed software interfaces. Currently, databases and tools provided by BROP include: (i) a graphical genome viewer (Genome Viewer) that allows side-by-side visual comparison of independently annotated datasets for the same genome; (ii) a pipeline of automatic data-mining algorithms to keep the genome annotation always up-to-date; (iii) comparative genomic tools such as Genome-wide ORF Alignment (GOAL); and (iv) the Oral Pathogen Microarray Database. BROP can also handle unfinished genomic sequences and provides secure yet flexible control over data access. The concept of providing an integrated source of genomic data, as well as the data-mining model used in BROP can be applied to other organisms. BROP can be publicly accessed at http://www.brop.org.


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