PriFi

PriFi designs degenerate PCR primer pairs from multiple-sequence DNA alignments to enable amplification of orthologous loci across phylogenetically related species when prior sequence information is limited.

Key Features:

• Comparative Approach: Uses alignments of DNA sequences from phylogenetically related species to identify conserved, likely orthologous regions.
• Degenerate Primer Design: Generates lists of potentially degenerate primer pairs optimized for cross-species PCR amplification of homologous sequences.
• Customizable Criteria: Allows specification of primer design parameters and configuration settings to tailor primer selection to experimental needs.
• Marker Development Automation: Automates identification of common anchor loci and initial steps for developing general cross-species markers.

Scientific Applications:

• Developing Cross-Species Markers: Produces primer sets for phylogenetic and population genetics studies requiring common genetic markers across species.
• Genomic Research: Assists in identifying conserved genomic regions for comparative and functional genomics analyses.
• Biodiversity Studies: Supports studies of genetic diversity and conservation across species when prior sequence data are limited.

Methodology:

Analyzes multiple-sequence DNA alignments from related species to identify conserved regions, then designs and outputs candidate degenerate PCR primer pairs.