Primers4Clades

Primers4Clades is a new web-based tool for PCR primer design. As taken from their website, "Primers for clades (Primers4Clades) is an easy-to-use web server for the design of PCR primers for cross-species amplification of novel sequences from metagenomic DNA or from uncharacterized organisms belonging to user-specified phylogenetic clades or taxa. It implements an extended CODEHOP primer design strategy based on both DNA and protein multiple sequence alignments of coding sequences. It evaluates several thermodynamic properties of the oligonucleotide pairs, as well as the phylogenetic information content of predicted amplicons, which is computed from the branch support values of maximum likelihood phylogenies. Trees displayed on screen make it easy to design taxon-specific PCR primers by selecting user-specified species or sequence clades. Lastly, the server also provides the alignments of the original input sequences used to compute the NJ tree, as well as those for the in silico amplicon sets obtained with each primer pair". Primers4Clades (primers for clades) is developed and maintained by Pablo Vinuesa at CCG/UNAM (Mexico) and Bruno Contreras-Moreira at EEAD/CSIC (Spain), with technical support provided by Romualdo Zayas-Laguna and Victor del Moral. The project is funded by grant DGAPA IN201806-2 from DGAPA/PAPIIT-UNAM, grant P1-60071 from CONACyT-Mexico, ARAID and by grant 200720I038 from CSIC. If you have any questions or suggestions on how to improve Primers4Clades, please feel free to email Pablo Vinuesa.