COnsensus-DEgenerate Hybrid Oligonucleotide Primers (CODEHOP)
The COnsensus-DEgenerate Hybrid Oligonucleotide Primers (CODEHOP) program (Rose et al. 2003, Nucleic Acids Research 31:3763-3766) is hosted by the Fred Hutchinson Cancer Research Center in Seattle, Washington and designs PCR (Polymerase Chain Reaction) primers from protein multiple-sequence alignments. The program is intended for cases where the protein sequences are distant from each other and degenerate primers are needed. The multiple-sequence alignments should be of amino acid sequences of the proteins and be in the Blocks Database format. Proper alignments and Blocks Database formatting can be obtained by different methods at the website. The result of the CODEHOP program are suggested degenerate sequences of DNA primers that you can use for PCR. You have to choose appropriate primer pairs, get them synthesized and perform the PCR to see how well they work. This program proved to be highly successful in identifying "universal degenerate" primers capable of amplifying informative genes from diverse bacterial lineages (see Santos and Ochman ) for ecological and evolutionary analyses.