[BiO BB] Designing degenerate primers

Cook, Malcolm MEC at Stowers-Institute.org
Thu Feb 23 11:41:39 EST 2006

Vector NTI's  (windows only) AlignX module supports your needs quite
nicely (though not in a high throughput fashion).  Version 10 is now
free to academics (!), though getting registered is a bit of a bear.  
Some researchers here at the Stowers Institute used it for amping up a
lizard gene based on chicken aligned with (was it?) mouse.  For further
specificity, they designed nested degenerate primer pairs (if I remember
AlignX can import precomputed alignments too (but only in MAF format).
Let us know what you do.
The following is from their Help file, and might help you decide if the
weighty install is worth your effort:

	The Alignment PCR feature in Vector NTI allows you to design PCR
primers for amplifying a region of aligned DNA/RNA molecules. Using this
feature, you can design primer pair sets that will amplify any of the
DNA/RNA molecules in a specified alignment. In this type of PCR
analysis, the molecules are first aligned in AlignX and the alignment is
subsequently analyzed using the Alignment PCR feature in Vector NTI.
	The basic procedure for performing an Alignment PCR analysis
consists of the following steps:
	1. Define the set of DNA/RNA molecules you want to use for
Alignment PCR analysis.
	2. Align the set of molecules in AlignX.
	3. Select a region of the AlignX alignment for which Alignment
PCR will be run.
	4. Define the Alignment PCR parameters.
	5. Perform the Alignment PCR analysis.

>From another page in the help file (Alignment PCR parameters), I quote

	Primer/Every Molecule Set the minimum overall similarity and 3'
end similarity for the primer with every molecule in the alignment


Malcolm Cook - mec at stowers-institute.org
<mailto:mec at stowers-institute.org>  - 816-926-4449
Database Applications Manager - Bioinformatics
Stowers Institute for Medical Research - Kansas City, MO  USA 



bio_bulletin_board-bounces+mec=stowers-institute.org at bioinformatics.org
[mailto:bio_bulletin_board-bounces+mec=stowers-institute.org at bioinformat
ics.org] On Behalf Of Maximilian Haeussler
	Sent: Wednesday, February 22, 2006 7:56 PM
	To: The general forum at Bioinformatics.Org
	Subject: Re: [BiO BB] Designing degenerate primers
	forgot to forward to the list: 
	you don't have to do the sequences alignment yourself. on
genome-test.soe.ucsc.edu <http://genome-test.soe.ucsc.edu/> you'll find
multiple alignments of 12 mammalian species (switch on track "MultiZ 10
way" or "MultiZ 12 way"). You can extract alignments with "Table
Browser" - "MultiZ 10 Way" - Download as maf (or fasta?). 
	Take care,
	On 22/02/06, Nagesh Chakka < nagesh.chakka at anu.edu.au
<mailto:nagesh.chakka at anu.edu.au> > wrote: 

		Hi all,
		I need to design primers to "fish out" the region of
interest from 
		reptilian genomic sequence. I donot have the reptilian
gDNA sequence
		information to design the primer with exact sequence.
Hence I thought of
		designing degenerate primers based on the available
sequence information 
		(eutherian mammal, marsupial, amphibian). Are there any
		programs which does this kind of primer design or that I
need to perform
		a multiple sequence alignment and look for the most
conserved region and 
		design primer with that.
		Any advice is greatly appreciated.
		Bioinformatics.Org general forum  -
BiO_Bulletin_Board at bioinformatics.org
<mailto:BiO_Bulletin_Board at bioinformatics.org> 

	Maximilian Haeussler, 
	CNRS Gif-sur-Yvette, Paris
	tel: +33 6 12 82 76 16
	icq: 3825815  -- msn: maximilian.haeussler at hpi.uni-potsdam.de
<mailto:maximilian.haeussler at hpi.uni-potsdam.de>  
	skype: maximilianhaeussler 

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