[EMBOSS] is it possible to use emboss without writing a full application?

[Daily, Jeff A]

EMBOSS Community,

I’ve looked at the example application “seqret” and I think I understand it well enough.  However, I am more interested in being able to programmatically call the “needle” application without a system call.  More specifically, I would like to simply use emboss’s NW alignment function *without* writing a full application.  I guess another way to ask this is, I have a completely different way of gathering command-line user input that doesn’t use Ajax/ACD, can I still use emboss for sequence alignment?  That’s the kind of example I need.  Any help is appreciated.  Thanks.

_______________________________________________
Jeff Daily
Scientist
DATA INTENSIVE SCIENTIFIC COMPUTING GROUP

Pacific Northwest National Laboratory
902 Battelle Boulevard
P.O. Box 999, MSIN K7-90
Richland, WA 99352 USA
Tel: 509-372-6548
Fax: 509-372-4720
jeff.daily at pnnl.gov
www.pnnl.gov