[Bioperl-l] Retrieving update sequence from GenBank

Brian Osborne osborne1 at optonline.net
Mon Sep 4 12:20:09 EDT 2006


Ryan,

Bio::DB::SeqVersion is designed to do this:

    use Bio::DB::SeqVersion;

    my $query = Bio::DB::SeqVersion->new(-type => 'gi');

    # all GIs, which will include the GI used to query
    my @all_gis = $query->get_all(2);

    # the most recent GI, which may or may not be the GI used to query
    my $live_gi = $query->get_recent(2);


Brian O.


On 9/4/06 1:14 AM, "Ryan Golhar" <golharam at umdnj.edu> wrote:

> I'm using Bio::DB:GenBank::get_Seq_by_id passing in the GI:76628052.
> The record has been replaced by GI:78369420 (NP_001030432).
> 
> Is there any way to determine if a sequence has been replaced, and what
> its replacement ID is, or follow the replacement tree to get the latest
> sequence?  
> 
> Ryan
> 
> 
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