Fwd: primer design guide

---------- Forwarded message ----------
From: John Cumbers <johncumbers@gmail.com>
Date: Sun, Apr 25, 2010 at 1:45 AM
Subject: Fwd: primer design guide
To: Mackenzie Cowell <macowell@gmail.com>, diybio@googlegroups.com


Hi Mac,
I've started using geneious for primer design, it uses primers3 but
with a nicer interface.  I know you can make primers with the 30 day
free trial and maybe after that with the limited version.   Genious is
a really nice tool in general for organizing and playing around with
sequences, although for high throughput stuff it is not the right
tool.
 http://www.geneious.com/

Cheers,
John

---------- Forwarded message ----------
From: Nathan McCorkle <nmz787@gmail.com>
Date: Tue, Apr 20, 2010 at 8:17 PM
Subject: Re: primer design guide
To: Cory Tobin <cory.tobin@gmail.com>, diybio <diybio@googlegroups.com>


Thanks,
the square brackets fixed things as far as getting the coding sequence
inside the primers... now do you know if there is a way to tell it
specifically where to start and stop? or should I just remove the UTR
regions if I don't want to prime on them?
can you tell me if I need to be concerned with removing or chopping
the untranslated regions? What are their purposes? I am thinking of
ligating this cDNA into a vector that has a his-tag or a translocation
sequence (if I use it in yeast for secretion).
Again thanks a lot, great stuff to know (even though I could have got
it out of a prof in 5 minutes, its gonna stick with me now for sure)
-Nathan

On Tue, Apr 20, 2010 at 11:06 PM, Cory Tobin <cory.tobin@gmail.com> wrote:
>
> On Tue, Apr 20, 2010 at 7:06 PM, Nathan McCorkle <nmz787@gmail.com> wrote:
> > Still isn't working... ugh I did exactly what you said but it just keeps
> > pushing the start primer forward in the sequence, and the end primer is
> > getting pulled further into the sequence.... I'm really not sure why, this
> > system seems like it needs a redesign, or I'm just really missing something.
> > Any more help?
>
> Oh my bad, square brackets, not curly brackets.
>
> Yeah, the site isn't very web2.0ish.  Pretty much the exact opposite.
> Although, they do a good job of describing what each of the parameters
> does (if you click on the links) and how to use them.  It's just not
> blatantly obvious how everything works.
>
> Btw, the code is GPL so anyone can use it to make their own
> new-and-improved primer picker.  I'm sure people have, I'm just not
> aware of them.
>
>
> -Cory



--
Nathan McCorkle
Rochester Institute of Technology
College of Science, Biotechnology/Bioinformatics

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