CODEHOP

CODEHOP designs consensus-degenerate hybrid oligonucleotide primers for PCR amplification of distantly related gene sequences to detect conserved amino acid motifs and enable discovery of gene orthologs, paralogs, and novel pathogen species.

Key Features:

• Design strategy: Integrates conserved blocks of amino acids derived from multiply-aligned protein sequences to target conserved regions when nucleotide sequence homology is low.
• Primer structure: Produces primers with a 3' degenerate core encoding 3–4 highly conserved amino acids and a longer 5' non-degenerate clamp containing the most probable nucleotides predicted from flanking codons.
• Primer pool generation: Outputs a pool of related primers to accommodate sequence variability at the degenerate core while maintaining clamp-driven specificity.
• Integration with Blocks Database tools: Leverages BlockMaker and the Multiple Alignment Processor within the Blocks Database for identification and use of conserved protein blocks.

Scientific Applications:

• PCR amplification of divergent genes: Enables amplification of distantly related gene sequences across gene families with low nucleotide identity.
• Conserved motif isolation: Facilitates isolation of sequences encoding conserved amino acid motifs from divergent genes.
• Ortholog and paralog discovery: Assists in identifying new gene orthologs and paralogs across taxa.
• Pathogen identification: Supports detection and characterization of novel pathogen species in plants, animals, and bacteria.

Methodology:

Identify conserved amino acid blocks from multiple protein alignments; design primers with a 3' degenerate core (encoding 3–4 amino acids) and a 5' non-degenerate clamp using predicted nucleotides from flanking codons; generate pools of related primers; integrate BlockMaker and the Multiple Alignment Processor from the Blocks Database.