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Help- degenerate primer design - (Dec/08/2006 )

Hi,

I need help about primer design. Can someone recommend a good software for degenerate primer design?

Thank

Alice

-sisma-

QUOTE (sisma @ Dec 8 2006, 10:21 AM)
Hi,

I need help about primer design. Can someone recommend a good software for degenerate primer design?

Thank

Alice


Why do you need degenerated primers??
I used any normal design program (vector NTI, for example) and then I make the changes I consider by my self.

If some one knows a free software, I want it too!!! biggrin.gif

A+C+G V
A+C+G+T N
A+T+G D
T+C+G B
A+T+C H
A+T W
C+G S
T+G K
A+C M
C+T Y
A+G R

-aztecan princess-

yeah i have always designed them myself for identifying related genes,

make a clustal sequence alignment to identify your regions of homology and chose a couple that would give a product fo 300-600 bp (this depends how big you want to go)

now look at changing some codons, take care to not introduce too much degeneracy into your primers otherwise you might get lots of bands!!!

1 fold sites M W
2 fold sites F Y H Q N K D E C
3 fold sites I
4 fold sites V P T A G
6 fold sites L S R


hope this helps

-Jimmy_september-

Have a look at http://bioinformatics.weizmann.ac.il/blocks/codehop.html

One of my students had some success with CODEHOP primers.

-wbla3335-

Yes Codehop is good, also you could download a free copy of MEGA 3.1, to form and align a block to roughly look at the conserved regions. The Data from Mega ca nalso be fed into the CODEHOP block maker.
All the best

-nifT-