Vector contamination

frist at ccu.umanitoba.ca frist at ccu.umanitoba.ca
Sat Jul 17 12:22:15 EST 1993


In article <CAB8ry.I0H at ms.uky.edu> woodward at seqanal.mi.uky.edu (Jerry Woodward) writes:
>If the vector sequences are now annotated, that means they know they are
>there.  Why don't they remove the damn things!  Kind of makes you
....other stuff deleted
>
>Jerry Woodward
>Univ. of Kentucky
>
Unfortunately, it's not that simple. (You knew I was going to say that.)
I believe that the majority of the
vector contamination features were discovered by the database staff using
similarity search programs. While the coordinates you get from such
a search give you a pretty good idea of where the vector sequence is, they
can't be trusted as the precise end points for defining where does vector
end and where does insert begin. The only way that I can see to remove
these things is if you knew the vector and cloning site and therefore the
precise vector/insert junctions. The authors are best suited for this task
and should be informed by the databases when vector contamination is 
found.

It gets fuzzier. Some vector contamination appears WITHIN a sequence!
This is likely the result of sequencing subcloned fragments from within
a larger fragment, and bringing along the border fragments. You would
think that if the thing was sequenced even twice in that region that
the vector region would cause contig assembly programs to flag it.
Maybe that says something both about contig assembly programs, as well
as the lax attitudes some people have about sequencing.

Anyway, the bottom line is that each case of vector contamination is a
special case that requires human intervention to do the dissection
properly.

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