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