Design and implementation of a database for Brucella melitensis genome annotation

Area of Science:

• Genomics
• Bioinformatics
• Microbial Pathogenesis

Background:

• Availability of genome sequences for Brucella species and related organisms enables new relationship analyses.
• Manual correction of Brucella melitensis genome annotation by experts improved accuracy of open reading frames (ORFs).

Purpose of the Study:

• To create a publicly accessible, functional, and auto-updatable database (alphaPAGe) for the corrected Brucella melitensis genome.
• To integrate diverse genomic data, including predicted functions, biochemical properties, and phylogenetic comparisons.

Main Methods:

• Manual curation of 3198 open reading frames (ORFs) in the Brucella melitensis genome, involving 899 start site modifications.
• Development of the alphaPAGe database using an entity-relationship (ER) approach and a multi-purpose structure.
• Implementation of a user-friendly graphical interface with three query levels: basic, advanced (combining criteria), and SQL.

Main Results:

• Creation of alphaPAGe, a comprehensive database for the corrected Brucella melitensis genome.
• The database integrates results from automatic annotation tools and BLAST comparisons against 9 related Brucella genomes.
• Advanced search functionalities allow queries based on function, physicochemical properties, structural criteria, and phylogenetic similarity.

Conclusions:

• alphaPAGe provides a valuable resource for researchers studying Brucella melitensis and related species.
• The database facilitates in-depth analysis of bacterial genomics, function, and evolution.
• Public accessibility via a web server enhances data sharing and collaborative research in microbial genomics.