[Bioperl-l] seq features with locations on remote entries?

[Hilmar Lapp]

All locations have a property $loc->is_remote(). The property 
$loc->seq_id() gives what ultimately is supposed to serve as a URI or 
LSID, but probably in most cases in just going to be the accession 
number, possibly in accession.version notation.

Quoted from the POD in Bio::LocationI:

        is_remote

         Title   : is_remote
         Usage   : $is_remote_loc = $loc->is_remote()
         Function: Whether or not a location is a remote location.

                   A location is said to be remote if it is on a 
different
                   'object' than the object which 'has' this
                   location. Typically, features on a sequence will 
sometimes
                   have a remote location, which means that the location 
of
                   the feature is on a different sequence than the one 
that is
                   attached to the feature. In such a case, $loc->seq_id 
will
                   be different from $feat->seq_id (usually they will be 
the
                   same).

                   While this may sound weird, it reflects the location 
of the
                   kind of AB18375:450-900 which can be found in 
GenBank/EMBL
                   feature tables.

hth,

	-hilmar

On Friday, July 4, 2003, at 09:55  AM, Matthew Betts wrote:

>
> Hi,
>
> Are the Bio::SeqFeature and Bio::Location objects able to handle 
> sequence
> features with locations on an entry other than the one to which the
> feature belongs? (As described in item 7 of section '3.4.12.2 Feature
> Location' of ftp://ftp.ncbi.nih.gov/genbank/gbrel.txt) If the feature 
> is a
> coding sequence, for example, can the translation of the entire thing 
> be
> retrieved?
>
> If so, please could you tell me how (or where to look)? Thanks.
>
> Sorry if this is obvious, or has been answered else where; I couldn't 
> see
> any mention of it in the documentation.
>
> Thanks,
>
> Matthew
>
> -- 
> Matthew Betts, mailto:matthew.betts at ii.uib.no
> Phone: (+47) 55 58 40 22
> Computational Biology Unit, BCCS,
> University of Bergen, N-5020 Bergen, Norway
>
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-- 
-------------------------------------------------------------
Hilmar Lapp                            email: lapp at gnf.org
GNF, San Diego, Ca. 92121              phone: +1-858-812-1757
-------------------------------------------------------------