[BiO BB] Withdrawl of Refseq accessions

Ryan Golhar golharam at umdnj.edu
Tue Jun 6 17:02:18 EDT 2006

XM_ sequences are predicted sequences.  I would not rely on them as they
have not been verified.  
NM_ sequences are RefSeq sequences, and are much more stable - They are
the NCBI curated sequences and have evidence supporting them.
In some cases, you can do from the XM_ sequences to the GeneID to the
new NM_ sequence that represents that Gene.  I think the XM_ GenBank
entry also documents the new NM_ entry.

-----Original Message-----
From: bio_bulletin_board-bounces+golharam=umdnj.edu at bioinformatics.org
[mailto:bio_bulletin_board-bounces+golharam=umdnj.edu at bioinformatics.org
] On Behalf Of Michael Muratet US-Huntsville
Sent: Tuesday, June 06, 2006 11:53 AM
To: bio_bulletin_board at bioinformatics.org
Subject: [BiO BB] Withdrawl of Refseq accessions

I recently discovered that about 3000 Refseq accessions that were
present in the 4/2005 release have been withdrawn. The ones I've looked
at appear to be NCBI predictions using their gnomon tool and had 'XM_*'
accessions. I'm concerned that a database that is supposed to be stable
is so dynamic. I asked NCBI about it, but didn't get an explanation.
Does anybody have any experience with such large scale withdrawls? Does
anybody know why?

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