CAPRIB

CAPRIB performs comparative analyses of proteins at the genus level to identify amino acid changes associated with phenotypic divergence in bacteria.

Key Features:

• Database Integration: Utilizes SQL databases to manage and compare multiple bacterial genomes.
• Phenotypic Correlation Analysis: Narrows down amino acid changes that are concomitant with phenotypic differences between two groups of organisms at the genus scale.
• Statistical Evaluation: Associates each identified permutation of amino acid change with statistical values indicating its potential impact on protein function.
• Evolutionary Insights: Detects known and novel mutations and highlights molecular phylogeny and mechanisms such as point mutation, gene deletion, duplication, or insertion of foreign DNA.

Scientific Applications:

• Mycobacterial phenotype evolution: Identification of amino acid changes that coincide with the emergence of slow-growing mycobacteria from fast-growing counterparts.
• Evolutionary hotspot identification: Highlighting candidate pathways, such as the cytokinin pathway, for further experimental investigation.

Methodology:

Performs phylogenetic and genomic comparisons across bacterial genera, uses SQL-based genome management to compare sequences, and applies statistical evaluation to permutations of amino acid changes linked to phenotypic divergence.