Oligo 4.0-s program (how to adjust parameters)

HARDIES at THORIN.UTHSCSA.EDU HARDIES at THORIN.UTHSCSA.EDU
Mon Mar 13 12:10:32 EST 1995


SPAGNOL at PLAUTO.CSATA.IT wrote:

> Is just my impression or the program [OLIGO 4.0] 
excessively severe? If I do a combined search, 9 time out of ten 
the program does not find two primers which could give a reasonable 
probability of success. I use the program default parameters.

For automated searching, you have to customize the search parameters. 
For most purposes, try limiting the portion of the oligo to be tested
for dimers down to the last 6 or so bases on the 3' end.  Check you
final choice of primer pair with the other options.  If necessary you
could ease up on loop delta G, as long as you keep the loop Tm about
10 degress below the intended priming temp.  You can ease up on the
Terminal stability limit if you don't intend to use the primers for
sequencing, and if the template isn't very complex, or if your
experiment isn't threatened by a few spurious bands at other  sizes. 
The unique 3' end limit triggers a search with all the sequence that
you have loaded, so if you load a lot of extraneous flanking seq.,
this will unnecessarily limit your finds.

No affiliation to the program vendors.

Hope this helps.
Steve Hardies, Assoc. Prof. of Biochem., Univ. of Texas HSC at San
Antonio
Hardies at uthscsa.edu




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