Primer design strategy?

Darren Natale dnatale at box-d.nih.gov
Wed Feb 19 09:17:23 EST 1997


hcorbett at garnet.berkeley.edu wrote:
> 
> There must be a simple, standard way to do this; please make suggestions:
> 
> I would like to go fishing for expression of members of a broad family of
> enzymes in my animal system. I was able to figure out how to search
> GenBank, EMBL etc. in order to create a file on my unix account which
> contains a couple hundred of this type of enzyme. But I really don't know
> how to use this software (the GCG stuff, which looks ever so powerful
> and daunting)!
> 
> How do I align these sequences so as to find common domains, from which I
> could make some degenerate oligonucleotides in order to do RT-PCR? For
> that matter, is it reasonable to hope to amplify any fragments to use
> in screening a library afterwards? But the main problem is trying to
> design the primers. Software recommendations would be greatly appreciated
> (e.g. BLAST or DNA Strider or GEneworks?).

You can use GCG's PILEUP program.  For an easy way to read GCG
documentation,
point your web browser to:

http://molbio.info.nih.gov/molbio/molbio_docs/gcg/

I find this easier than using GENHELP.

D. Natale



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