[Bioperl-l] Fuzzy Locations and GenBank

Hilmar Lapp hlapp at gmx.net
Sat Aug 19 00:08:26 EDT 2006


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
>
>
>
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>

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: Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
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