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Old 08-13-2012, 02:51 AM   #1
rsingh2083
Junior Member
 
Location: delhi

Join Date: Aug 2012
Posts: 4
Unhappy Where can i find the protein accesion id list on ncbi.

Hi all ,
I need to download some random samples of protein sequences in FASTA format.
So where can i find the list of all the protein sequence sequence accession ids(of all the proteins ) on NCBI.
I have downloaded gene2accession from ftp://ftp.ncbi.nih.gov/gene/DATA/
and GbAccList.0304.2012 from ftp://ftp.ncbi.nih.gov/genbank/livel...t.0304.2012.gz .
But Im totally confused about the difference between the two.

From ftp://ftp.ncbi.nlm.nih.gov/genbank/l...bank.livelists

Protein accessions can be easily distinguished from nucleotide accessions because they have a three-letter prefix, followed by five digits. The remaining accessions are nucleotide accessions, in either a one-letter/five-digit format or a two-letter/six-digit format.
So I tried this

Code:
cat GbAccList.0304.2012  | sed -n '/^[[:alpha:]][[:alpha:]][[:alpha:]][[:digit:]]/p' | head
OUTPUT

Code:
EBA53284,1,134307104
EBA53285,1,134307105
EBA53286,1,134307106
EBA53287,1,134307107
EBA53283,1,134307103
EBA53288,1,134307109
EBA53289,1,134307110
EBA53290,1,134307111
EBA53291,1,134307113
EBA53292,1,134307114
But all of these are givin this error on NCBI : protein ::

"Database is not supported: protein"

So where are the protein sequence id's then ??

Last edited by rsingh2083; 08-13-2012 at 02:53 AM.
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