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

frist at ccu.umanitoba.ca frist at ccu.umanitoba.ca
Fri Jul 16 16:40:38 EST 1993


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,
and the email server performs a search on all annotation, you get any
entry that in any way refers to the sequence you requested. So when I
tried retrieving with Lambda's unique accession number (J02459) I got
so many vector-contaminated sequences that it exceeded the line limit that
I had set at what I thought was a conservatively high figure, before it
even got to Lambda itself!

The purpose of this posting is not to gripe at NCBI. I have already sent
suggestions to them on how I think this problem might be overcome. What 
I want to do here is vent my spleen about sloppy sequencing!

How can you not know that your sequence contains vector? You know who you
are; yes I'm talking to YOU! Yes you over there with the 32P all over 
your hands -- are you so sloppy that you don't even bother to look
for the BEGINNNING of your insert on each and every sequencing run?
You know where you cloned the damned thing, you know the exact sequence
of the polylinker, or the internal primer. What do you do, just read
lane after lane into a bunch of computer files and ask a STUPID (there is
no other kind) program to put together something for you?

There is no excuse for the kind of slovenliness that we're seeing more
and more in sequencing strategies. YOU SHOULD BE ASHAMED OF YOURSELVES!
DON'T YOU KNOW YOUR NAMES ARE ON THESE PAPERS AND WILL BE IN THE 
DATABASE FOR CENTURIES? IS THAT HOW YOU WISH TO BE REMEMBERED?
AREN'T YOU EMBARRASSED? WHERE DID YOU LEARN TO SEQUENCE, ANYWAY? AT KMART?

There are three choices:
      1. People begin to clean up their acts.
      2. We throw up our collective hands and go into investment banking.
      3. We throw up. 

Ahhhhhhh. That feels better. 
 
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Brian Fristensky                | 
Department of Plant Science     |  A question is like a knife that slices
University of Manitoba          |  through the stage backdrop and gives us
Winnipeg, MB R3T 2N2  CANADA    |  a look at what lies hidden behind.
frist at ccu.umanitoba.ca          |  
Office phone:   204-474-6085    |  Milan Kundera, THE UNBEARABLE LIGHTNESS 
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