# CODEHOP:
COnsensus-DEgenerate Hybrid Oligonucleotide Primers

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## PCR primers designed from protein multiple sequence alignments

- Getting started
- Full Help file
- The CODEHOP algorithm
- The CODEHOP manuscript
- Genes identified using CODEHOP

- The input should be a set of local multiple alignments (blocks) of a group of related protein sequences. The alignments must be in Blocks Database format, such as in Block Maker
output.
- Ungapped parts of Clustal- or FASTA-formatted global multiple alignments can be automatically turned into blocks by the Blocks multiple alignment processor. You can also manually reformat multiple sequence alignments with the Blocks formatter.
- The output of all these programs contains links that send the resulting blocks to this page.
- If your sequences align globally, you will get better multiple alignment results from Clustal than from the motif finders used by Block Maker.
- Blocks are processed using sequence weights (the numbers following each sequence segment). To emphasize particular sequences in the block(s) manually adjust the sequence weights. Increase the number to give a sequence more weight.

Paste your block(s) below: |

Core (degenerate 3' region) | - degeneracy [default=128]: |  |
| - strictness [default=0.0]: |  |
Clamp (non-degenerate 5' region) | - temperature [default=60.0]: |  |
| - poly-nuc [default=5]: |  |
Primer concentration [in nM, default=50nM]: |  | ([K+]=50mM)

Genetic code

Codon usage table (scroll for more choices):

By default, up to 3 of the least degenerate primers in an overlapping set are shown.

Show the least degenerate, or show all overlapping primers.

By default, the 3' base of the primer must be an invariant position, regardless of the core strictness setting.
Use core strictness for the 3' base.

Force the core/clamp boundary to be a codon boundary. Use the most common codons in the clamp.

[Blocks home] [CODEHOP help] [Getting started] [CODEHOP program]

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Page last modified <MODIFICATION_DATE>Mar 2003</MODIFICATION_DATE>