Primer design strategy?

hcorbett at garnet.berkeley.edu hcorbett at garnet.berkeley.edu
Wed Feb 19 06:30:48 EST 1997

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?).



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