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PRIME and primer listing files

E. Hack mbeh at s-crim1.dl.ac.uk
Tue Dec 20 12:20:42 EST 1994


I am unable to use a file specifying possible primers with the GCG program
PRIME.  The program loads in the primers (or at least, identifies how many
there are), but apparently fails to test them.  Below is an example of the
sort of output I get; genosys.dat is a GCG file, so it ought to be in the
correct format!

I'd be grateful if anyone can suggest whether there is anything I might be
doing wrong or tell me if there is a bug in the program.  My apologies if I
am making an obvious mistake.

Thanks,

Ethan Hack                                  |  E-mail: Ethan.Hack at ncl.ac.uk
Dept. of Biological & Nutritional Sciences  |  Phone:  +44 91 222 8576
University of Newcastle                     |  Fax:    +44 91 222 8684
Newcastle upon Tyne  NE1 7RU, UK

------------------------------------------------------------------------------
PRIME of: nturf13.gcgn  ck: 1357  from: 1 to: 679  December 20, 1994 16:55


                                 INPUT SUMMARY
                                 -------------

    Input sequence: nturf13.gcgn
 Input primer list: genosys.dat with 2391 primers.

 Primer constraints:
    primer size: 9 - 9
    primer 3' clamp: S
    primer sequence ambiguity: NOT ALLOWED
    primer GC content: 40.0 - 55.0%
    primer Tm: 10.0 - 65.0 degrees Celsius
    primer self-annealing. . .
       3' end: <   8.0    (weight:  2.0)
        total: <  14.0    (weight:  1.0)
    unique primer binding sites: not required
    primer-template and primer-repeat annealing. . .
       3' end: ignored
        total: ignored
    repeated sequences screened: none specified

 Product constraints:
    product length: 100 - 600
    product GC content: 40.0 - 55.0
    product Tm: 70.0 - 95.0 degrees Celsius
    duplicate primer endpoints: NOT ALLOWED
    difference in primer Tm: < 2.0 degrees Celsius
    primer-primer annealing. . .
       3' end: <   8.0    (weight:  2.0)
        total: <  14.0    (weight:  1.0)


                                           PRIMER SUMMARY
                                           --------------

                                     forward            reverse

 Number of primers considered:             0                  0

 Number of primers rejected for . . .
               primer 3' clamp:            0                  0
     primer sequence ambiguity:            0                  0
             primer GC content:            0                  0
                     primer Tm:            0                  0
      non-unique binding sites:            0                  0
         primer self-annealing:            0                  0
     primer-template annealing:            0                  0
       primer-repeat annealing:            0                  0

 Number of primers accepted:               0                  0


                                          PRODUCT SUMMARY
                                          ---------------

 Number of products considered:                     0

 Number of products rejected for. . .
                product length:                     0
            product GC content:                     0
                    product Tm:                     0
              product position:                     0
    duplicate primer endpoints:                     0
       difference in primer Tm:                     0
       primer-primer annealing:                     0

 Number of products accepted:                       0
    Number of products saved:                       0




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