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Designing degenerate PCR primers

Genome Biology20001:reports240

  • Received: 29 February 2000
  • Published:


The purpose of CODEHOP is to help in the design of degenerate PCR primers from protein sequence.


  • Degenerate Primer
  • Block Format
  • Related Protein Sequence
  • Output Page
  • Unaligned Sequence


The purpose of CODEHOP is to help in the design of degenerate PCR primers from protein sequence. Given a multiple alignment of a series of target proteins, CODEHOP will transform the amino-acid consensus sequence into a DNA consensus sequence, using a user-designated codon-usage table. This DNA consensus is used to design degenerate primers, which are useful for identifying new family members in the same species or for pursuing phylogenetic studies in related species.


Reporter's comments


The site was last modified in December 1998.

Best feature

The ease of moving from a series of unaligned sequences to a series of degenerate primers is impressive. The most time-consuming part is using the BLOCKMAKER program to align the sequences and determine the sequence blocks. Once that is finished, the primer generation step takes only seconds.

Worst feature

The need for the sequences to be in BLOCKS format is annoying, though there is a converter that will take a Clustal multiple sequence alignment and transform it into a BLOCKS format. Unless you have a lot of sequences, or a carefully hand-edited alignment, it's probably best to use the BLOCKMAKER program to generate the necessary starting file.

Wish list

It would be useful to have the option of choosing primers and have them evaluated for possible secondary structure problems, self-annealing or primer-pair compatibility.

Related websites

There are several PCR primer design sites, including Primer3, DoPrimer, and. None of these programs, however, helps with the design of PCR primers from protein sequence. In this regard, CODEHOP appears to be unique.

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