BROP

BROP integrates and harmonizes diverse genomic data to support comparative genomics, functional annotation, and gene expression analyses of oral pathogens.

Key Features:

• Graphical Genome Viewer: Enables visual side-by-side comparison of independently annotated datasets for the same genome to support comparative genomic studies.
• Automatic Data-Mining Algorithms: Continuously update genome annotations to maintain current and consistent annotation data.
• Comparative Genomic Tools (Genome-wide ORF Alignment, GOAL): Provides Genome-wide ORF Alignment (GOAL) for comparative analyses across oral pathogen genomes.
• Oral Pathogen Microarray Database: Stores microarray data to support gene expression studies, including comparisons of virulent and avirulent strains such as Porphyromonas gingivalis, and to examine gene content variation and chromosomal islands acquired via lateral gene transfer.
• Handling Unfinished Genomic Sequences: Supports analysis of incomplete or unfinished genomic sequences.
• Harmonization of Gene Identification and Functional Annotation: Addresses discrepancies among different gene identification schemes and functional annotation methods across databases.

Scientific Applications:

• Comparative Genomics: Side-by-side viewer and GOAL enable genome-wide ORF alignment and comparative analyses across oral pathogen genomes.
• Functional Annotation: Harmonization and automated updates facilitate consistent functional annotation across multiple databases.
• Gene Expression Analysis: The microarray database supports differential expression studies, including comparisons between virulent and avirulent Porphyromonas gingivalis strains.
• Detection of Lateral Gene Transfer and Chromosomal Islands: Comparative analyses and gene content comparisons enable identification of chromosomal islands acquired via lateral gene transfer.
• Analysis of Incomplete Genomes: Tools and data structures support analyses that include unfinished genomic sequences.

Methodology:

Integrates and harmonizes diverse genomic data sources; provides a graphical genome viewer for side-by-side comparison of independently annotated datasets; employs automatic data-mining algorithms to update genome annotations; implements Genome-wide ORF Alignment (GOAL) for comparative ORF analyses; hosts an Oral Pathogen Microarray Database for gene expression comparisons; supports analysis of incomplete genomic sequences.