[BiO BB] Designing degenerate primers

[Maximilian Haeussler]

To import sequences into vector NTI:
Yes, you can download the alignments from ucsc directly, but only in
maf-format. If you need them converted to fasta, you can do it manually if
it's only a few sequences (search-replace) or use a script maf2fasta which
does to conversion for you. (if you cannot find it, I also have written
python script that does it)

I quote from the genome-mailinglist at ucsc:


Hi Robert,

You may try the download the multiz program from:
http://www.bx.psu.edu/miller_lab/dist/multiz-tba-2005-04-28.tar.gz. In there
you can find a program called maf2fasta, which can convert MAF to FASTA
format.

regards,
Hong

----- Original Message -----
From: "Donna Karolchik" <donnak at soe.ucsc.edu
<http://www.soe.ucsc.edu/mailman/listinfo/genome>>
To: "Querfurth" <querfurt at molgen.mpg.de
<http://www.soe.ucsc.edu/mailman/listinfo/genome>>; <genome at
soe.ucsc.edu <http://www.soe.ucsc.edu/mailman/listinfo/genome>>
Sent: Friday, July 22, 2005 2:59 PM
Subject: Re: [Genome] MAF format


On 23/02/06, Maximilian Haeussler <maximilianh at gmail.com> wrote:
>
> 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,
> Max
>
> 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
> > _______________________________________________
> > Bioinformatics.Org general forum  -  BiO_Bulletin_Board at bioinformatics.org
> > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board
> >
>
>
>
> --
> 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




--
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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