Primer design from multiple alignment.

R. Jayakumar jakku at mrna.tn.nic.in
Wed Jan 26 04:13:57 EST 2000


   I just did what you asked for designing some 16SrRNA primers from a
multiple sequence alignment of 20 similar 16SrRNA genes of Bacillus.  It is
very simple
    1.  First do the multiple sequence alignment (a msf file)
    2. Generate a consensus sequence from the msf file
    3. Develop primers for the consensus sequence for the region you want
    I used GCG on a TruUnix machine for my purpose.  Pileup for the getting
the multiple sequence file.  Then pretty for getting the consensus sequence
from it. "PRIME" to design the primers for the consensus sequence.
    If you are not good at Unix or GCG you can send me the multiple sequence
file and I can do the job foryou.
CSIR- Senior Research Fellow
Dept. of Molecular Microbiology,
School of Biotechnology,
Madurai Kamaraj University,
Madurai - 625 021.
email: jakku at usaf.org
tel: +91-452-858471-374
efax: (603)-688-4665
web: http://members.tripod.com/~jakspage
"There is a possible even in imPOSSIBLE"

----- Original Message -----
From: <Bill_A_Nussbaumer at ms.bd.com>
To: <bio-software at hgmp.mrc.ac.uk>
Sent: Tuesday, January 25, 2000 1:40 AM
Subject: Primer design from multiple alignment.

> Bill A Nussbaumer at BDX
> 01/24/2000 03:09 PM
> Hi all,
> I'm trying to find a computer program, preferably Win32 compatible but
> Linux compatible that will identify optimal primer sequences for PCR based
on a
> multiple sequence alignment.  i.e.  If I align a set of sequences from a
> genus that have some variation, I would like to find the best primers to
> all members of the set.  Any ideas would be most appreciated.
> TIA,
> Bill Nussbaumer
> ---


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