[Bioperl-l] X.Y Fuzzy locations no longer supported in GenBank/EMBL/DDBJ

Chris Fields cjfields at uiuc.edu
Wed Oct 18 09:55:37 EDT 2006


Ding dong the witch is dead!  As announce previously, from the latest
GenBank release (156.0):

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1.3.8 Feature location syntax X.Y no longer supported

  The Feature Table has supported feature locations of the form 'X.Y', to
represent a base position which is greater or equal to X, and less than or
equal to Y. For example:

	misc_feature    1.10..20
	misc_feature    join(100..150,200.210..250)

  In the first example, the misc_feature starts somewhere between bases 1
and 10 (inclusive), and ends at basepair 20. In the second, the 51 bases
from 100..150 are joined together with a second basepair interval, which
could be anywhere from 200..250 to 210..250 .

  Although this syntax seems like a reasonable way to capture an uncertain
interval, it is used for features on a vanishingly small number of sequence
records, most database submission mechanisms don't support it, and the
meaning of its use in a join() context is not entirely clear.

  As of October 2006, this type of location is no longer supported.
Those records with features which utilize X.Y locations will be reviewed and
converted to a non-uncertain format.

-----------------------------------------------

EMBL/DDBJ formats are also dropping support for these 'fuzzy' locations.
Not sure about UniProt/SwissProt.

I guess we're keeping this in for backwards compatibility only, but how do
we handle any bugs that pop up related to this?  

Christopher Fields
Postdoctoral Researcher - Switzer Lab
Dept. of Biochemistry
University of Illinois Urbana-Champaign 




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