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CEMAsuite / Codon-Equivalent Multiple Alignment suite
Begins conservational analysis for PCR primer design at the protein level, allowing the user to design consensus primers capable of detecting homologous coding sequences even when low-to-moderate sequence information is available. CEMAsuite also condenses the wealth of information associated with multiple sequence alignments and presents them in an intuitive manner, allowing the user to quickly and effectively address degenerate primer design considerations. The goal of CEMAsuite is to aid in the design of minimum-degeneracy primer sets which are robust enough for the assay at hand, while retaining as much specificity and product homology as possible.
FAS-DPD / Family-Specific Degenerate Primer Design
A package to design degenerate primers for PCR. FAS-DPD is very strict in the search of conserved regions and minimizes the amount of degeneracy incorporated at this end. The software is designed to use multiple alignments of proteins or nucleic acids and constructs a consensus degenerate sequence from that, which is then used to design the putative primers. This tool allows a more efficient search for enzymes and other proteins with commercial or biotechnological importance, making for a faster and cheaper research process.
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