JE <jeanette.erdmann at t-online.de> wrote:
> I'm a very newbie regarding the Staden package. I'm wondering how I can
> define a reference sequence?
> can anybody give me some help?
I guess you are doing SNP detection, since I do not see how a reference
sequence could be useful in fragment assembly. The reference sequence
must be written in a file in EMBL format. I wished for and if not yet
present, you can "manually" add lines of type :
FT CDS 134..949
FT exon 134..473
(the "features" will be displayed as "tags" by gap4).
When you run pregap4, you must select the module
"Reference traces/sequences " and fill in the name of the file in the
"Reference Sequence" box.
Does this answer your question ?