genefisher2

genefisher2 designs degenerate PCR primers from multiple homologous sequences to enable amplification of conserved genes across related organisms.

Key Features:

• Automated Primer Design: Automates design of degenerate primers from a group of homologous gene sequences to target unknown or variable sequences.
• Transparency of Design Parameters: Exposes the design parameters used for primer selection, enabling inspection of factors affecting primer specificity and efficiency.
• Systematic Approach: Utilizes information from a family of homologous genes to design primers that account for sequence variability across related organisms.

Scientific Applications:

• Comparative Genomics: Identification and extraction of homologous genes across genomes to study sequence conservation.
• Evolutionary Biology: Investigation of gene conservation and divergence across related species.
• Functional Genomics and Gene Family Characterization: Identification and characterization of gene families via PCR amplification using degenerate primers.

Methodology:

Analyzes sets of homologous sequences to identify conserved regions suitable for primer binding and generates degenerate primers that account for sequence variability among those homologues, relying on conserved sequence motifs resulting from functional conservation.