PhyloPrimer

PhyloPrimer designs taxon-specific oligonucleotides (PCR primers) for targeted detection of genes and organisms in environmental and biomedical microbiome samples.

Key Features:

• Dynamic Sequence Retrieval and Alignment: Retrieves GenBank gene sequences, aligns them, and constructs phylogenetic trees to represent sequence relationships for sequence selection.
• Taxon-Specific Oligo Design: Implements a positive/negative consensus approach to distinguish targeted and non-targeted sequences and maximize specificity down to the species level.
• Comprehensive Validation Checks: Performs nearest-neighbor (NN) calculations for secondary-structure assessment, runs in silico PCR tests to detect potential off-target matches, and supports oligos with degenerate bases.
• Versatile Design Modes: Supports designing primers without taxonomic specificity, designing from preselected sequences, and validating predesigned oligos.

Scientific Applications:

• Environmental and Biomedical Biomonitoring: Enables targeted PCR detection of specific microorganisms or genes in complex microbiome samples for environmental and biomedical studies.
• Functional Gene Surveys: Supports exploration of specific gene functionalities within complex microbial communities.
• Primer Validation and Assay Development: Facilitates validation of predesigned oligos and development of taxon-specific PCR assays.

Methodology:

Retrieves GenBank sequences, performs sequence alignment, constructs a tree-based representation of phylogenetic relationships, applies a positive/negative consensus approach for oligo selection, computes nearest-neighbor (NN) thermodynamics for secondary-structure assessment, and runs in silico PCR to identify off-target matches while supporting degenerate bases.