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Hybridization Probes

Chris Botka botka at CGL.UCSF.EDU
Thu Sep 4 19:44:48 EST 1997


I don't think there is anything in GCG or in EGCG aside from prime.  
 We have primer3 and OSP installed, but they're not too popular  
around here.  You can goto:  
http://www.ebi.ac.uk/biocat/Oligomer_design_and_synthesis.htm to  
check out what is available there - a pretty long list.  Most of the  
programs seem to be designed to do PCR rather than hybridization.

We have a person here that uses a program called hybsimulator and  
loves it.  It's unfortunately $$.  you can check it out at:

http://www.hybsimulator.com/

MacVector has a kinda neat feature that scans protein sequences for  
Hyb probes, but does not tell you anything about secondary  
structure or alternate binding sites.

Good Luck.

Chris


STAFFA at niehs.nih.gov ("NICK STAFFA 361-5444 EXT. 410") wrote on 4  
Sep 1997:
> Does anyone have any experience using GCG to pick out probes for
> hybridization? Prime comes to mind, but my client seems to find it
> unsatisfactory.
>
> Nickolas G. Staffa
> National Institute of Environmental Health Sciences
> Research Triangle Park, North Carolina


______
Christopher W Botka			Phone: (415)476-5379
Sequence Analysis Consulting Service	Fax: (415)502-1755
UCSF Computer Graphics Lab		Office: Lib-111
Internet: botka at cgl.ucsf.ed		Mail Drop: Box 0446
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