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quotation of database entries, software etc.

khofmann at biomed.biolan.uni-koeln.de khofmann at biomed.biolan.uni-koeln.de
Fri Jan 15 03:24:31 EST 1993

Perhaps this is a little bit off the topic, but i have been considering
the following problems for quite a time now:

1. Teh first problem will be known to a big number of sequencing scientists:
Suppose you published a sequence in a database as GENBANK or EMBL. I have
the impression that one could as well publish it in a wastebasket unless
you have an paper on this sequence published in a 'real' journal.
By reading all those seqeunce-containing papers in even the most prestigeous
journals you get the feeling that the authors do check the databases for
similar or identical proteins or DNA. Everyone writes something like:
'A search of available DNA data bases revealed no significant homology...'
'A search of GENBANK rel. XX revealed this and that...'
But you mostly read such phrases if nothing was found with the database
searches. But what do authors do, if somebody else has in fact cloned
a similar/identical cDNA/gene? If it has been published on paper, one
usually doesn't get around citing it. But if it is onlyin some database,
there are many workarounds:
Besides the old trick of searching outdated databases, here are some more
elaborate ways
- 'A search of current sequence databases revealed no significant homology
   to previously published sequences'  
- 'Databae searches indicate that this protein is not homologeous to any
   identified protein of mammalian origin' (Nature)
   (forget about this 80% identical rat protein with only putative function)
- 'A search of DNA databases revealed no overall similarity to previously
   identified sequences' (better not check PIR/SwissProt, might find
   something there..)

But seriously, are there some guidelines of how to assure that authors
1) have checked appropriate and current databases
2) mention it if they found something
And, how should sequence data base entries be cited anyway?

Since sequencing is becoming kind of trivial these days and many journals
discourage publishing papers with focus on sequencing, publishing sequences
in a database ought to be encouraged. But I will not be in favour of this
approach as long as nobody feels the need of even mentioning your work.

With best regards,
                   Kay Hofmann

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