Hello,

You may try out iCODEHOP (COnsensus-DEgenerate Hybrid Oligonucleotide Primers), HYDEN (HighlY DEgeNerate primers), genefisher2, FAS-DPD, and CEMAsuite.

http://athena.bioc.uvic.ca/virology-ca-tools/codehop/

https://sourceforge.net/projects/cemasuite/

https://sourceforge.net/projects/fas-dpd/

http://bibiserv.techfak.uni-bielefeld.de/genefisher2/

http://acgt.cs.tau.ac.il/hyden/HYDEN.htm

If you're committed to using only web-based application, Primer3 is fairly decent (http://primer3.wi.mit.edu/).

Thanks Dioga.

What about the other methods of designing degenerate primers.

Please let me know.

u can use NCBI's primer designer also. But Primer3Plus seems to the best till now..

I used iCODEHOP http://dbmi-icode-01.dbmi.pitt.edu/i-codehop-context/

The interface was somewhat awkward, but in the end it worked well. And most importantly, the primers worked

I would suggest to use Primer 3 Plus instead of Primer 3. The former have more user friendly interface. As for "degenerate" primers, I usually use one sequence to get the primer pairs first. Subsequently, I would position the selected primer with the output of multiple sequence alignment and identify the degenerate points based the the aligned sequences. There should be a way to do that (i.e. identify the degenerate sites) automatically, but somehow I have not been able to use it. Good luck.

dear my friend

please use the NTI vector software or Prime 3 plus. 

Hello,

You may try out iCODEHOP (COnsensus-DEgenerate Hybrid Oligonucleotide Primers), HYDEN (HighlY DEgeNerate primers), genefisher2, FAS-DPD, and CEMAsuite.

http://athena.bioc.uvic.ca/virology-ca-tools/codehop/

https://sourceforge.net/projects/cemasuite/

https://sourceforge.net/projects/fas-dpd/

http://bibiserv.techfak.uni-bielefeld.de/genefisher2/

http://acgt.cs.tau.ac.il/hyden/HYDEN.htm

Thank you.

How to list out all possible primer sequences from a degenerate primer sequence? Any help would be appreciated.