[Genome] Primers from alignments (was: Trying to plan conserved primers)

[Maximilian Haeussler]

Hi Noa,

I've had this problem before as well, finally did it manually.  You
can try to convert the alignments from the ucsc website to fasta
format. Then, standard plasmid construction packages from CLC bio or
Vector NTI from Invitrogen include functions like this, both tools are
free of charge, available for Windows.
You can  run genefisher
http://bibiserv.techfak.uni-bielefeld.de/genefisher2/ onto them.

Others:
http://www.umsl.edu/services/kellogg/primaclade.html
http://cgi-www.daimi.au.dk/cgi-chili/PriFi/main?config.x=101&config.y=30

cheers
Max

2008/4/24 Noa Sher <sher at wi.mit.edu>:
> Hi,
>
>  I am trying to plan a set of primers for RT-PCR that I will optimally be
>  able to use for four species of Drosophila I am working on.
>  I can see the alignments of Drosophila but was wondering if other than
>  nit-picking by hand, is there any software I can use to plan primers
>  according to certain Tm restrictions using multiple alignments?
>
>  Thanks
>  Noa
>
>  --
>  Noa Sher
>
>  Postdoctoral Fellow
>  Laboratory of Terry Orr-Weaver
>  Whitehead Institute
>  9 Cambridge Center
>  Cambridge, MA 02142
>  Work: 617-258-6182
>  Cell: 617-710-6795
>
>
>  _______________________________________________
>  Genome maillist  -  Genome at soe.ucsc.edu
>  http://www.soe.ucsc.edu/mailman/listinfo/genome
>



-- 
Maximilian Haeussler,
tel: +33 6 12 82 76 16