On Fri, Mar 23, 2012 at 11:15 AM, Jeswin <phillyj101@gmail.com> wrote:
> On Fri, Mar 23, 2012 at 8:03 AM, Pat <eleten@gmail.com> wrote:
>> Check it out when you get a chance: http://www.ncbi.nlm.nih.gov/guide/howto/design-pcr-primers/
>>
> Looking at the site, it seems that it checks the primer that you have
> already built against the database. We need the opposite. We design
> the primer based on the most common mutations for the WT sequence site
if that's the case, don't you want to do an alignment of all the
possible sequences for your gene, the few highest scoring alignments
would seem to be the primer you want. (are you doing PCR, or is this
for hybridization/blot assays?)
--
Nathan McCorkle
Rochester Institute of Technology
College of Science, Biotechnology/Bioinformatics
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