SIMON@geneseo.bitnet (BOB SIMON) (03/13/91)
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
***************************************************************
Robert D. Simon Internet: simon@genva.cc.geneseo.edu
Professor and Chairman Bitnet: SIMON@GENESEO.BITNET
Department of Biology Phone: (716) 245-5301
SUNY-Geneseo FAX: (716) 245-5007
Geneseo, NY 14454
U.S.A.
***************************************************************JMILLER%VXBIO.SPAN@STAR.STANFORD.EDU (03/13/91)
A mac program for this is being written by the same group that produced MapMaker, an extremely sophisticated program for genetic linkage analysis. The program will not only do the normal thermodymanic calculations, but is smart enough to tell whether you will get hybridization to known repetitive sequences in the organism you are working with! I'll post more when I find out about it. -Peter Markiewicz