Hi,
as a simple biologist I find the trivial problem below overwhelming. I
would be extreamly grateful for any help.
I am sequencing a few thousand plasmids from a substraction cDNA library to
find a few hundred novel unique genes of interest. The substractions and
cloning have included 3 different restriction enzymes. If the ligations
would have worked optimally every plasmid would contain only one cDNA
fragment. As they have not about one third of the plasmids contain several
different cDNA fragments separated by one of the 3 restriction sites. How
can I separate these fragments from each other before the
assembly/consensus sequence forming stage? Or is there a way to separate
them some how automatically in GAP or a like program based on the presence
of the restriction site? So far I have been using pherd for base calling
and Staden after that.
Best regards,
Mikko Arvas
VTT Biotechnology - Research Scientist
e-mail: mikko.arvas at vtt.fi
tel: +358-(0)9-456 5827
mobile: +358-(0)50-381 0502
fax: +358-(0)9-455 2103
mail: Tietotie 2, Espoo
P.O. Box 1500
FIN-02044 VTT, Finland
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