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defining a refence sequence

Guy Bottu gbottu at black.vub.ac.be
Tue Dec 16 10:09:31 EST 2003

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?
> Jeanette

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 ?

        Guy Bottu

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