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  • 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, 01:53 AM.

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