sequence quality in eprimer3

[Guy Bottu]

from  : BEN

I am afraid that the EMBOSS "wrapper" program eprimer3 does not handle the base 
assignment qualities, even if the manual briefly mentions it. Actually, EMBOSS 
does not handle Staden experiment files. If you ask seqret to write 
experiment::xxx it writes a sequence in the now obsolete Staden format.
(let's not blame the developers, it is such a monumental task to implement 
everything...)

You might install primer through its "native" interface, using the 
primer3_www.cgi script. This is more rich than EMBOSS, but is of course 
"featureless" (no access to personal files on the server). You still will have 
to extract "manually" the content of the AV lines and copy-and-paste in the 
"Sequence Quality" box.

	Regards,
	Guy Bottu