microarray primer design

Gary Williams, Tel 01223 494522 gwilliam at hgmp.mrc.ac.uk
Thu Mar 20 09:28:20 UTC 2003

Microarrays typically use oligos of about 50 to 60 bp in length.

The maximum length of an oligo that can be found by the primer3 program
is 35.
This limit is governed by the maximum oligo size for which primer3's
melting-temperature is valid.


Thomas Keller wrote:
> I've always designed primers one at a time. Usually with the very
> excellent program Oligo (W. Rychlik).
> I've got eprimer3/primer3 working but I'm not sure how to use it to
> find hybridization oligos for use with microarrays.
> I'd be grateful for suggestions, since I've got about 1,300 oligos to
> design.
> Thanks,
> Tom K.

Gary Williams               Tel: +44 1223 494522  Fax: +44 1223 494512
mailto:G.Williams at hgmp.mrc.ac.uk            http://www.hgmp.mrc.ac.uk/
Bioinformatics,MRC HGMP Resource Centre,Hinxton,Cambridge, CB10 1SB,UK

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