Designing PCR primers

[Paul St. Amand]

In article <476cgt$oiu at ds2.acs.ucalgary.ca>, tlpalmer at acs5.acs.ucalgary.ca
(Taunja Lee Palmer-Stone) wrote:

PSt> Is there a Mac freeware/shareware programme for designing PCR primers? 
PSt> (and if there is where can I find it).  I have two sequences that I would 
PSt> like to use as primers in a bacteria which favours G/C in its codon 
PSt> usage.  Since I am using two consensus sequences I am somewhat limited in 
PSt> my choice of primer sequences.  I know people who have had mixed 
PSt> experiences with designing PCR primers.  Some didn't check  
PSt> their primers and later couldn't get their PCR to work because the two 
PSt> primers didn't anneal at the same temperature.  Others didn't check and 
PSt> got good results (different primers of course).  Which scenario is the 
PSt> most prevalent?  I would like to check my proposed primers before I get 
PSt> them synthesized.  Any PCR gurus out there with advice/comments?  Also, 
PSt> are there any pitfalls to using I in PCR primers?

Taunja:

Here are some of the free-ware programs available for molecular biology on
the Mac. Let me know if you run across others!

I use Primer and OSP to design primers. They work well, if you add in a
little experience. Amplify is great for double-checking newly designed
primers.

Good luck!
Paul St. Amand

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Primer
(New Mac version due any time now!)

Get it at...
ftp://genome.wi.mit.edu/distribution/software/

or to use a Unix version via the web...

http://www-genome.wi.mit.edu

***********************************************************************
 OSP
(Not available by ftp. You MUST contact the author.)

Get it at...
email: lfw at elegans.wustl.edu

***********************************************************************
Oligo Analyzer
(I don't know of an ftp site for this. Contact author.)

Get it at...
email: jcuozzo at opal.tufts.edu

***********************************************************************
HyperPCR

Get it at...
ftp://ftp.bio.indiana.edu/molbio/mac

***********************************************************************
Amplify

Get it at...
ftp://ftp.bio.indiana.edu/molbio/mac

***********************************************************************
Other Mac MolBio stuff that you will likely need at some point. These ftp
pointers are to specific files but you should also see what else each
directory has in it.

ftp://ftp.bio.indiana.edu/molbio/align/clustalw.hqx
ftp://ncbi.nlm.nih.gov/pub/schuler/macaw/mac-68k/macaw2.0.5.sea.hqx
ftp://evolution.genetics.washington.edu/pub/phylip/phylipmx.sea.hqx
ftp://evolution.genetics.washington.edu/pub/phylip/phylippmac.sea.hqx
ftp://ftp.virginia.edu/pub/fasta/mac/fasta20u3.cpe.bin
ftp://iubio.bio.indiana.edu/molbio/seqpup/mac/seqpup-mac-68k.hqx
ftp://iubio.bio.indiana.edu/molbio/seqpup/mac/seqpup-mac-ppc.hqx
ftp://iubio.bio.indiana.edu/molbio/seqpup/mac/seqpup-mac-apps.hqx
ftp://iubio.bio.indiana.edu/molbio/seqapp/seqapp.hqx

Paul C. St. Amand    (PST at KSU.KSU.Edu)
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