[Bioperl-l] Fuzzy Locations and GenBank

Heikki Lehvaslaiho heikki at sanbi.ac.za
Thu Aug 24 09:17:27 EDT 2006


On Monday 21 August 2006 05:55, Steve Chervitz wrote:
> I imagine EMBL and DDBJ will follow suit in banishing fuzzy locations
> as well. Anyone know?

Yes, all three db will do the change. This is a change in the Feature Table 
which can not be touched unless all three collaborating sequence databases 
agree.

	-Heikki

> Steve
>
> On Aug 18, 2006, at 9:08 PM, Hilmar Lapp wrote:
> > Great, the fewer fuzzy locations the better. -hilmar
> >
> > On Aug 19, 2006, at 12:03 AM, Chris Fields wrote:
> >> 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
> >>
> >>
> >>
> >> _______________________________________________
> >> Bioperl-l mailing list
> >> Bioperl-l at lists.open-bio.org
> >> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> >
> > --
> > ===========================================================
> >
> > : Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
> >
> > ===========================================================
> >
> >
> >
> >
> >
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>
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-- 
______ _/      _/_____________________________________________________
      _/      _/
     _/  _/  _/  Heikki Lehvaslaiho    heikki at_sanbi _ac _za
    _/_/_/_/_/  Associate Professor    skype: heikki_lehvaslaiho
   _/  _/  _/  SANBI, South African National Bioinformatics Institute
  _/  _/  _/  University of Western Cape, South Africa
     _/      Phone: +27 21 959 2096   FAX: +27 21 959 2512
___ _/_/_/_/_/________________________________________________________


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