PangenePro

PangenePro automates the identification and classification of gene family members across multiple plant genomes through integrated sequence alignment, domain validation, and orthologous clustering.

Key Features:

• Multi-genome analysis: Identifies and classifies gene family members across multiple genomes simultaneously.
• Sequence alignment: Uses BLAST for sequence alignment.
• Domain validation: Validates domains through InterProScan.
• Orthologous clustering: Classifies identified genes into core, dispensable, and unique pangene sets.
• Cross-species validation: Tested on Arabidopsis thaliana, Arachis, rice, and Barley genomes.

Scientific Applications:

• Gene family identification: Enables genome-wide identification of gene families across multiple plant genomes.
• Intraspecific diversity studies: Captures intraspecific genetic diversity through multi-genome comparison.
• Plant breeding research: Yields candidate genes for functional and plant breeding studies.

Methodology:

The pipeline uses Python and R scripting implemented in the Linux environment, integrating BLAST for sequence alignment, InterProScan for domain validation, and orthologous clustering to classify genes into core, dispensable, and unique pangene sets.