restriction digest discrepancies from vector polymorphisms?

Ask questions about sequence improvement / finishing D. mojavensis projects here.
Post Reply
cjones
Posts: 99
Joined: Sun Feb 04, 2007 10:19 pm
Location: Moravian College, Bethlehem PA
Contact:

restriction digest discrepancies from vector polymorphisms?

Post by cjones » Tue Mar 13, 2007 6:21 pm

Most of my students are seeing discrepancies between the real and in silico digests of their fosmids. However, in almost every case it's a question of a single fragment spanning an insert/vector junction being 2 fragments in the other case; the discrepant position is always in the vector. Sometimes the single fragment is in the "real" digest and sometimes in the in silico. Are others seeing this, and should I tell students to ignore it? I understand the issue of polymorphisms within the Drosophila DNA, but I'm nonplussed about this within the vector.
Chris Jones
Assoc. Prof. of Biology
Moravian College
Bethlehem PA

cjones
Posts: 99
Joined: Sun Feb 04, 2007 10:19 pm
Location: Moravian College, Bethlehem PA
Contact:

Post by cjones » Tue Mar 13, 2007 6:24 pm

Never mind, I just re-read Chuck Hauser's thread on the same issue. To which I had (embarrassingly) already replied. Unfortunately, we just got off spring break, so I'm not sure what excuse I've got.
Chris Jones
Assoc. Prof. of Biology
Moravian College
Bethlehem PA

Post Reply