Juniper - gene design for the masses

Introduction: For an introduction to Juniper, see this page.

Important: As juniper is currently an experimental program, it is not yet available on general release. Please do not give the URL to anybody else.

Disclaimer: Juniper is an experimental program. It is about as robust as a puff pastry suspension bridge. Getting it to produce silly results is undoubtedly very easy, especially if you miss out parameters or use nonsensical values. Above all, CHECK YOUR RESULTS.

Feedback: If Juniper isn't working as you would expect or you're having problems using it, contact Chris Richardson.

Citing Juniper: If you use Juniper in your work, please cite our paper on the recursive PCR process. Prodromou, C. & Pearl, L. H. Protein Engineering, 5, 827-829 (1992).

Protein sequence (in FASTA format):

Optional preceeding base sequence (just bases, no punctuation):

Optional succeeding base sequence (just bases, no punctuation):

Codon usage threshold for eliminating overlap:

Codon usage threshold for eliminating multiple restriction:

Codon usage threshold for excluding banned enzymes:

Codon usage threshold for adding restriction sites:

Maximum permitted overlap:

Optimum annealing temperature (°C):

Permitted slop in annealing temperature (°C):

Optimum oligo length:

Permitted slop in oligo length:

Smallest gap suitable for restriction site:

Lower limit for small gap after insertion of restriction site:

Codon usage:

E. coli
Yeast

Restriction enzymes:

Sticky ended 6-cutters
Prod's cutters
Rana's cutters

Banned enzymes:

Juniper was written by Dr Chris Richardson, and is based on the Recursive PCR process of Professor Laurence Pearl and Dr Chris Prodromou. Thanks to Dr Chris van der Walle for helpful discussions.

Last updated 20 March 2000.