OLIGO v1.0
                           
OVERVIEW:

Oligo is a user-rpl program to calculate the melting temperature of
DNA-DNA or DNA-RNA hybridization for use in PCR and northern/southern
blotting. For those who don't know, the melting temperature of a
nucleotide sequence is the temperature at which two strands of DNA
separate from one another, or "denature". The algorithm used is the one
in the reference section of the 1996 New England Biolabs catalog.

OPERATION:

The program takes a string in level 1 consisting of the nucleotide
sequence in terms of A, T, G, C, and U. Orientation is irrelevant for
melting temperatures so it doesn't matter if you enter the sequence
from 5'-3' or 3'-5'. Any characters other then A, T, G, C or U are
ignored so sequences may be formatted with spaces, carriage returns,
numbers and what not. 

Two variables may also be present in the same directory as the oligo
program but are not necessary: 

        'Na' - The monovalent salt concentration of the buffer.
        
        '%FORM' - The percent formamide in the buffer.

If either of these variables is not present when the program is run,
they are created with the default values Na=.33 and %FORM=0. Those
are the values that I use in my protocol. I believe they are also
the same as in Maniatis et al.

When the program is called with the string on the stack it displays 
on the screen:

          -The molecular weight of the (single-stranded) oligonucleotide
           sequence in daltons.

          -The GC content as a percentage.

          -The length in nucleotides.

          -The Oligo-Oligo melting temperature for the sequence in
           degrees celsius: The oligo-oligo melting temperature is the
           temperature at which two oligonucleotides denature. It is
           almost, but not quite equal to, that of an oligo annealing
           to a full strand.

          -The DNA-DNA melting temperature in degrees celsius.
           (for southern blotting, PCR, etc.)

          -The RNA-RNA melting temperature in degrees celsius.

          -The DNA-RNA melting temperature in degrees celsius.
           (used mostly for northern blots).

Hit any key to exit. The program leaves nothing on the stack.

EXAMPLE:

         1:  "GATACAGATA GCGCGCAAAA ATGCTAGTCA ACTGATCGTA AAAAAAAAAA"

         -> oligo (called with default values of Na and %FORM.

                   Mol Wt: 15792 daltons
                   GC Content: 31.5%
                   Length: 54
                   Oligo   Tm=62.5^C
                   DNA-DNA Tm=62.53^C
                   RNA-RNA Tm=57.06^C
                   DNA-RNA Tm=54.72^C


COMMENTS:

This program gave the same results as the oligo calculator on Pedro's
biomolecular tools homepage (at least for the random sequences I typed
into it). 

                                   Dan Beamish
                                   beamish@yorku.ca