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. 2005 Jul 1;33(Web Server issue):W734-40.
doi: 10.1093/nar/gki361.

The bioinformatics resource for oral pathogens

Tsute Chen  1 , Kevin Abbey, Wen-jie Deng, Meng-chuan Cheng
Affiliations

The bioinformatics resource for oral pathogens

Tsute Chen et al. Nucleic Acids Res. .

Abstract

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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Figures

Figure 1
Figure 1
Screen shot of the Genome Viewer software (A) showing side-by-side comparison of annotations from multiple sources for the same region of the genome P. gingivalis W83. The clickable links in the viewer are depicted with the rectangular callout boxes: (B) TIGR CMR; (C) LANL Oralgen; (D) NCBI; (E) BROP Gene Summary; (F) Array Amplicon Information; and (G) OPMD.
Figure 2
Figure 2
Visualization of whole-genome ORF alignment between the genomes of P.gingivalis W83 and Bacteroides thetaiotaomicron VPI-5482 using the GOAL tool. Actual display of the forward and reverse matches was shown in blue and red colors, respectively.
Figure 3
Figure 3
Screen shot of the Genome Explorer software (A) showing a plethora of tools and information available for a particular gene selected. The interface contains links to (B) a text-based annotation searching result; (C) a summary page for individual ORF; (D) the Genome Viewers; (E) Gene Ontology information; and (F) KEGG metabolic pathway.
Figure 4
Figure 4
Pipeline of automatic annotation of oral pathogen genomes.
See this image and copyright information in PMC

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