Software and PCR

BOB SIMON SIMON at geneseo.bitnet
Tue Mar 12 22:26:00 EST 1991


   I have not seen much discussion on computer programs to aid in
the use of PCR technology.  Because I do not have easy access to
a DNA synthesizer and must choose my primers with some care, I am
particularly interested in help determining the most appropriate
PCR primers for a defined gene sequence.

  a. Is there software (commercial or shareware [via ftp?]) which
     will help in choosing the best primers?

  b. Several of the books I have read refer to the programs
     "Squiggles" and "Circles" which can be used to look at
     nucleic acid secondary structure so that regions with such
     structures can be avoided.  Are these programs available by
     ftp?

  c. I have the sequences for a series of homologous genes and
     would like to determine whether there is a single set of
     primers which could be used to identify the gene from
     different strains of bacteria.  While there are many
     multiple sequence alignment programs available, are there
     any would be particularly useful in identifying consensus
     nucleotide sequences and help with the primer selection?

   I use IBM's but would consider using a Mac or UNIX machine if
there was a particularly useful program available.

   Since there is obviously wide spread interest in PCR, I will
share any results of this inquiry with the BIO-SOFT community.


Thanks:  Bob Simon

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Robert D. Simon          Internet: simon at genva.cc.geneseo.edu
Professor and Chairman     Bitnet: SIMON at GENESEO.BITNET
Department of Biology       Phone: (716) 245-5301
SUNY-Geneseo                  FAX: (716) 245-5007
Geneseo, NY   14454
U.S.A.
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