nohup_Primer_& ??

Heikki Lehv{slaiho Heikki.Lehvaslaiho at Helsinki.FI
Tue Apr 14 02:41:48 EST 1992

In article <1992Apr14.001432.24351 at magnus.acs.ohio-state.edu>, gchacko at magnus.acs.ohio-state.edu (George W Chacko) writes:
> Has anyone ever run background jobs with Primer (the Eric Lander version) 
> in the Unix environment? If so tell me how please. When the program
> compares 700 forward and backward primers it can take a while.

When you have entered all the input and the program starts crunching, 
press CTRL-Z to suspend it:

[1]  + 18441 Suspended              primer

The number in square brackets shows you the number of the job. Next at 
your normal UNIX prompt, type bg to start running the process at the 
background. If you want it back to the foreground type fg. If you have 
several processes running simultaneously, add the number to the command. 
Command jobs shows all your jobs.

I have done this several times, but there really are so many potential 
primer pairs always available that I find it best to restrict severely 
the criteria by which primers are selected. Start by lowering the allowed 
number of complementary nucleotides (both to themselves and to each other) 
and using at least two nucleotides long 3' GC clamp. Also, determining 
strictly the target, subsequence and/or product length greatly speeds up the 
calculation. You probably get better primers, too. Remember, it's always 
possible to loosen the criteria if your first run didn't find any primers.

Hope this helps,


Heikki Lehv{slaiho  <Heikki.Lehvaslaiho at Helsinki.FI>
Meilahti Medical Departments, University of Helsinki
Haartmaninkatu 3, SF-00290 Helsinki, FINLAND
Phone: +358-0-434 6408         FAX: +358-0-434 6491

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