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  • Blast Database selection

    Database selection:

    What is the difference of the database 'Nucleotide collection (nr/nt)' and 'NCBI Genome (Chromosome)'?

    Thanks?

  • #2
    Originally posted by arkilis View Post
    Database selection:

    What is the difference of the database 'Nucleotide collection (nr/nt)' and 'NCBI Genome (Chromosome)'?

    Thanks?
    nr/nt is is all entries from traditional divisions of GenBank, EMBL, and DDBJ excluding gss, sts, pat, est, htg, and wgs.

    Before today I had never head of "NCBI Genome (Chromosome)". I suspect it's a subset of nt that only includes sequences from "fully" sequenced chromosomes. Refseq_genomic would then be a subset of "NCBI Genome (Chromosome)" only including sequences with "refseq" status.

    That's my guess..

    edit. I'm probably wrong..

    Title:Nucleotide collection (nt)
    Description:The nucleotide collection consists of GenBank+EMBL+DDBJ+PDB+RefSeq sequences, but excludes EST, STS, GSS, WGS, TSA, patent sequences as well as phase 0, 1, and 2 HTGS sequences. The database is partially non-redundant. In some cases identical sequences have been merged into one entry, while preserving the accession, GI, title and taxonomy information for each entry. Merged sequences include GenBank and RefSeq entries with identical sequences. Sequences added to the database since April, 2011 have also been merged with identical existing entries.
    Molecule Type:mixed DNA
    Update date:2013/09/19
    Number of sequences:19746987
    Title:NCBI Chromosome Sequences
    Molecule Type:Genomic
    Update date:2013/09/16
    Number of sequences:37566
    Title:NCBI Genomic Reference Sequences
    Molecule Type:mixed DNA
    Update date:2013/08/12
    Number of sequences:3149238
    Last edited by rhinoceros; 09-19-2013, 11:04 PM.
    savetherhino.org

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    • #3
      Originally posted by rhinoceros View Post
      nr/nt is is all entries from traditional divisions of GenBank, EMBL, and DDBJ excluding gss, sts, pat, est, htg, and wgs.

      Before today I had never head of "NCBI Genome (Chromosome)". I suspect it's a subset of nt that only includes sequences from "fully" sequenced chromosomes. Refseq_genomic would then be a subset of "NCBI Genome (Chromosome)" only including sequences with "refseq" status.

      That's my guess..

      edit. I'm probably wrong..

      Thanks, you are really helpful.

      Comment

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