[BiO BB] Designing degenerate primers

Maximilian Haeussler maximilianh at gmail.com
Wed Feb 22 20:56:28 EST 2006

forgot to forward to the list:
you don't have to do the sequences alignment yourself. on
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> 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 available
> 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.
> Thanks
> Nagesh
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Maximilian Haeussler,
CNRS Gif-sur-Yvette, Paris
tel: +33 6 12 82 76 16
icq: 3825815  -- msn: maximilian.haeussler at hpi.uni-potsdam.de
skype: maximilianhaeussler
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