[Bioperl-l] Fuzzy Locations and GenBank

Chris Fields cjfields at uiuc.edu
Sat Aug 19 00:03:01 EDT 2006


Don't know how much this will affect Bio::Location::Fuzzy, but I  
thought it might be worth a heads-up in case something pops up:

 From the latest GenBank release (154.0):

...

1.4.6 Feature location syntax X.Y to be discontinued

   The Feature Table currently supports feature locations of the
format 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 will no longer be
supported. Those records with features which utilize X.Y locations
will be reviewed and converted to a non-uncertain format prior to
that date.


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





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