Primaclade

Primaclade applies Primer3 to multiple-species nucleotide alignments to identify PCR primers suitable for cross-species amplification and analysis of sequence conservation.

Key Features:

• Primer3 integration: Uses the Primer3 primer-design algorithm to generate candidate PCR primers from input sequences.
• Iterative per-sequence analysis: Applies Primer3 iteratively to each sequence within the provided multiple-species nucleotide alignment file.
• Cross-species primer identification: Identifies primers predicted to bind across diverse species represented in the alignment.
• Aggregation of results: Collects and consolidates primer candidates generated from each sequence analysis.
• Alignment recapitulation: Includes a recapitulation of the original nucleotide alignment alongside primer results.
• Consensus sequence generation: Derives a consensus sequence from the input alignment.
• Per-region primer listings: Lists primers tailored to specific regions within the alignment.
• Degeneracy annotation: Annotates primers by level of degeneracy and represents degeneracy information in the output.

Scientific Applications:

• Evolutionary biology: Enables design of primers for amplifying conserved loci across taxa to study evolutionary relationships.
• Phylogenetics: Supports primer selection for multi-species sequence sampling in phylogenetic analyses.
• Comparative genomics: Facilitates identification of conserved regions and comparative genetic analyses across species.
• Molecular assay development: Assists molecular biology experiments requiring cross-species amplification and assessment of sequence conservation/divergence.

Methodology:

Iteratively applies Primer3 to each sequence in the input multiple-species nucleotide alignment, aggregates primer candidates, derives a consensus sequence from the alignment, and lists primers per alignment region with degeneracy annotation.