From stdabb14 from shsu.edu  Mon Jul 16 13:56:30 2007
From: stdabb14 from shsu.edu (Anna B. Buchman)
Date: Mon Jul 16 17:09:28 2007
Subject: [Genetic-linkage] Primer Design for Microsatellites
Message-ID: <3385.158.135.197.110.1184612190.squirrel@sammail.shsu.edu>

Hi,
I'm in the process of developing microsatellite primers to study box
turtle hybridization, and I am now at the initial stage of actual primer
design. Any recommendations as to what software is best for designing
primers for microsats? I'm currently exploring Invitrogen's Vector NTI and
B. Fairthcloth's Msatcommander (works off of primer 3.) Also, any advice
on what is the best way to process and analyze samples once the microsat
regions are ID'd and primers are designed? I'm going to need to do a few
hundred samples, and our facilities do not have a functional sequencer.
What companies out there do cheap AFLP analysis? Thanks.

From stdabb14 from shsu.edu  Wed Jul 25 15:00:21 2007
From: stdabb14 from shsu.edu (Anna B. Buchman)
Date: Wed Jul 25 18:53:29 2007
Subject: [Genetic-linkage] Primer Design for Microsatellites
Message-ID: <2824.158.135.188.13.1185393621.squirrel@sammail.shsu.edu>

Hi,
Thanks for all the replies to the previous posting, guys. I have now
ordered the primers, and have a commercial sequencing question. I plan to
fluorescently tag the primers when I verify that they work, and am looking
to send the resulting tagged PCR products to a company that can do an
AFLP/microsatellite variability assay on them, since we don't have an
automated sequencer and I would like to avoid manually running and
analyzing sequencing gels. What companies can provide that service for a
reasonable price? Also, if I do end up doing it myself, any ideas on how
to simplify the procedure overall? Anything radioactive is out of the
question, but I have read others doing silver staining with polyacrilamide
gels rather than flourescent tagging, and even running agarose gels.
Thanks.