[Bioperl-l] Missing Sequences

[Brian Osborne]

Mick,

Those NM_* ids correspond to RefSeq entries. From the FAQ:

  Q2.3: How can I get NT_ or NM_ accessions from NCBI (Reference
	Sequences)?

	Use Bio::DB::RefSeq not Bio::DB::GenBank when you are retrieving
	the NM_ accessions. This is still an area of active development
	because the data providers have not provided the best interface for
	us to query.  EBI has provided a mirror with their dbfetch system
	which is accessible through the Bio::DB::RefSeq object however,
	there are cases where NT_ accessions will not be retrievable.


Brian O.

-----Original Message-----
From: bioperl-l-admin@bioperl.org [mailto:bioperl-l-admin@bioperl.org]On
Behalf Of Mick Watson
Sent: Thursday, May 30, 2002 11:30 AM
To: bioperl-l@bioperl.org
Subject: [Bioperl-l] Missing Sequences

This is an old-ish problem when using Bioperl to fetch multiple
sequences from GenBank/EMBL

I am using EMBL.pm (Bioperl 1.0) to fetch multiple sequences that have
been identified from a blast search against Unigene.  Parsing the
Accession from unigene entries is simple as I just look for the

    /gb=.....

token and I have the accessions.  Simple.

The problem is, I guess, that these are GenBank accessions so I get the
following list:

AL117415 AJ291674 AJ291673 AJ291675 NM_022139 AF253318 NM_025220
AB055891 BI826766 BG547620

When I use EMBL.pm to fetch these, it croaks with the error that
NM_022139 and NM_025220 do not exist, and when I try to fetch them from
the ebi, it's right, they don't.  However, when I go to the NCBI, they
DO exist in GenBank (or at least the NCBI's nucleotide fetch tool says
that they do)

So my question is why is it that there are sequences in GenBank that
aren't in EMBL?  I'm guessing the NM_ prefix has some sort of
relevance....

Also, this looks as if this will force me to use GenBank.pm to fetch the
sequences and not EMBL.pm, and I don't want to do this for various
reasons....

Thanks
Mick

_______________________________________________
Bioperl-l mailing list
Bioperl-l@bioperl.org
http://bioperl.org/mailman/listinfo/bioperl-l