CODEHOP (COnsensus-DEgenerate Hybrid Oligonucleotide Primer) PCR primer design
What you can do:
Design degenerate PCR primers based on multiple protein sequences alignments.
Highlights:
- This is a new primer design strategy for PCR amplification of distantly related gene sequences based on consensus-degenerate hybrid oligonucleotide primers.
- CODEHOPs are used in PCR amplification to isolate distantly related sequences encoding the conserved amino acid sequence.
- 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.
- CODEHOP performs exclusively at the amino acid level and tries to identify all theoretically possible nucleic acid coding variants resulting from the degenerate genetic code. Thereby it does not, and does not attempt to, minimize the degeneracy of the primer.
- The CODEHOP designer is linked to BlockMaker and the Multiple Alignment Processor within the Blocks Database World Wide Web (http://blocks.fhcrc.org).
Keywords:
- PCR primers
- PCR primer design tool
- Polymerase Chain Reaction primers design tool
- degenerate primers
- degenerate primer design tool
- protein sequence alignments
- protein multiple sequence alignments
- consensus-degenerate hybrid oligonucleotide primers
Literature & Tutorials:
This record last updated: 01-03-2007