[Bioperl-l] GenBank updated sequence not being retrieved

Ryan Golhar golharam at umdnj.edu
Thu Jan 24 16:17:14 EST 2008


I'm using Bioperl 1.4 (and tried with 1.5.1).

I'm trying to download GenBank sequence for which I have accession #'s. 
  One of the sequences has been replaced with a newer version.  I'm 
using get_Seq_by_acc, which returns the warning:

-------------------- WARNING ---------------------
MSG: acc (gb|XM_087386) does not exist
---------------------------------------------------

If I check NCBI's website for the sequence, it has indeed been replaced 
by an NM_ sequence.  How can I get BioPerl to retrieve the latest 
version of a sequence?



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