UniPrime2

UniPrime2 automates the design of universal PCR primers by retrieving homologous sequences from GenBank, aligning them to identify conserved regions, and selecting primers for amplification of variable genomic regions.

Key Features:

• Automated Workflow: Accepts a gene reference ID or FASTA sequence, retrieves homologous sequences from GenBank, aligns them, and produces primers targeting conserved regions flanking variable sites.
• Integration of Multiple Tools: Integrates Blastn for homology retrieval, T-Coffee and GramAlign for multiple sequence alignment and conserved-region identification, and Primer3 for primer design.
• Phylogenetic Delimitation: Designs primers that are phylogenetically delimited to target conserved regions across defined evolutionary contexts (species or strains).
• Experimental Validation: Primers generated by the pipeline have been validated in wet-laboratory experiments.

Scientific Applications:

• Phylogenetic studies: Generation of universal primers for amplification of phylogenetic markers across multiple taxa.
• Comparative genomics: Amplification of homologous genomic regions to enable cross-species or cross-strain sequence comparison.
• Evolutionary biology: Facilitation of studies on sequence variation and evolutionary relationships by enabling cross-taxa amplification of variable regions.

Methodology:

Input a gene reference ID or FASTA; Blastn retrieves homologs from GenBank; T-Coffee or GramAlign performs multiple sequence alignment to identify conserved regions; Primer3 designs candidate primers.