GTACG

GTACG identifies homologous coding-sequence clusters and associates gene presence with user-defined phenotype groups across bacterial genomes to reveal genes potentially linked to adaptation and virulence.

Key Features:

• Phenotypic characteristic analysis: Identifies subgroups of bacterial genomes that share defined phenotypic characteristics and compares them to other groups.
• Homologous CDS cluster formation: Forms homologous clusters of coding sequences through local alignments.
• Subgroup-exclusive gene identification: Detects genes exclusive to specific microbial subgroups that may be linked to unique phenotypes.
• Data input formats and grouping: Accepts genomic files in FASTA and coding sequence files in CDS, faa, gbf, gb, and gff formats and uses user-defined phenotype groups.
• Validation on Xanthomonadaceae: Validated on 161 Xanthomonadaceae genomes, identifying 19 families of orthologous proteins present in 90% of plant-associated genomes associated with adaptation and virulence.

Scientific Applications:

• Comparative bacterial genomics: Associate gene presence-absence patterns with phenotypic traits across bacterial strains.
• Study of microbial adaptation and pathogenicity: Identify candidate genes linked to adaptation and virulence in plant-associated bacteria.
• Prioritization of molecular targets: Generate candidate gene families for downstream experimental validation in microbiology and plant pathology.

Methodology:

Formation of homologous coding-sequence clusters via local alignments using genome FASTA and coding-sequence files (CDS, faa, gbf, gb, gff), analysis of gene presence in user-defined phenotype groups, and validation on 161 Xanthomonadaceae genomes yielding 19 orthologous protein families in 90% of plant-associated genomes.