Vector contamination in seq. data (Self-righteous tirade)

David Mathog mathog at seqvax.caltech.edu
Sun Jul 18 14:23:00 EST 1993


In article <CAA1Jq.9t8 at ccu.umanitoba.ca>, frist at ccu.umanitoba.ca () writes...
>I just tried to retrieve the Lambda phage sequence from
>retrieve at ncbi.nlm.nih.gov.  I got back everything BUT Lambda!
>The reason is that vector contamination is now annotated in GenBank,
>...

Ok, I'll say the obvious - Genbank should stop flagging vector
contamination in new entries and instead reject such entries.

A lot of journals won't publish until they get the accession number(s).
Consequently, this policy would hold up publication (gasp!) and so give the
slobs a compelling reason to clean up their mess. 

Besides, the Genbank folks can't be expected to edit out vector
contamination.  As Brian noted, an entry's sequencers are the most familiar
with how a particular sequence was derived, and so are in the best position
to remove vector contamination. 

It would also make sense to have a policy that no sequence could be entered
into the database unless the vector it was cloned in was also entered, such
vectors being stored in separate vector division of Genbank.  This would 
make it easier to detect vector contamination from obscure vectors.

Anyway, that's my two cents worth,

David Mathog
mathog at seqvax.bio.caltech.edu
Manager, sequence analysis facility, biology division, Caltech



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