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

frist at ccu.umanitoba.ca frist at ccu.umanitoba.ca
Sat Jul 17 14:05:39 EST 1993


In article <CABKGL.DMG at usenet.ucs.indiana.edu> jgraham at bronze.ucs.indiana.edu (the End) writes:
>
>Brian,
>
>I'm not sure I read you on this one. What is the problem, retrieving sequences
>other than the desired one,
The problem I mentioned in my first
posting is that if you try to retrieve Lambda by accession # from
retrieve at ncbi.nlm.nih.gov, ANY entry with annotation referring to
Lambda, by accession number, will be retrieved. With the
newly introduced annotation of presumptive vector contamination,
 we're talking about a lot
of entries. Since there is a line limit on the data retrieved, unless 
you set a very high line limit as a search parameter, you won't even get
LAMBDA, because the entries are retrieved in alphabetical order according to
LOCUS name. One would imagine that the problem would be worse if you tried
to retrieve by name.

By the way, Barbara Rapp from NCBI pointed out a feature of the NCBI server
that I had forgotten about: You can limit your search to a specific field.
For example

J02459 [ACC]

would limit the search to the ACCESSION fields, which in this case should
return only LAMBDA.

 or entires wich do not have the corrrect genome
>sequence ? Are you saying that there are sequnces not found in Lambda phage
>contained within the Genebank file ?
>
>Jim
>
No, as far as I know, the true LAMBDA entry contains the correct sequence
and only the correct sequence.

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