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  • Naive issue of database download

    Hello All,

    I am trying to download the whole genome(nt) sequences for different species. But I don't get any single file for that.
    Eg I go to

    NCBI RefSeq FTP-> Genomes-> Homo sapiens
    ftp://ftp.ncbi.nih.gov/genomes/H_sapiens/

    The sequences are spread over different chromosomes.
    Should I download each chromosome and concatenate into one file or there is some other option?

    thanks,

  • #2
    Sheera, concatenating is one option.

    Depending on the species that you need, you might also find what you are looking for here:
    http://hgdownload.cse.ucsc.edu/downloads.html

    cheers!

    Comment


    • #3
      Thanks for the reply.
      But this concatenated dataset would serve as an database for the local stand alone blast+.

      I have to download almost all mammalian.
      Any better way of downloading the genomes.
      Thanks.

      Comment


      • #4
        Have you considered downloading pre-built blast index files from NCBI: ftp://ftp.ncbi.nlm.nih.gov/blast/db/

        Comment


        • #5
          Thanks GenoMax!
          But I am not agree I am not at itagain.
          I downloaded refseq_genomic_tar.gz data file from ftp://ftp.ncbi.nlm.nih.gov/blast/db/ like this

          ./update_blastdb.pl ftp://ftp.ncbi.nlm.nih.gov/blast/db/ refseq_genomic*

          I gunzip and got like 8 files as:
          refseq_genomic.nhr
          refseq_genomic.nin
          refseq_genomic.nid
          refseq_genomic.nnd
          refseq_genomic.nog
          refseq_genomic.nsi n more.
          I want to make this as file as my local database for the further blast thing.
          I have new blast ie blast+ working

          Now for formatdb, its makeblastdb.

          I dont know how the downloaded file works here as I tried many ways.
          ./makeblastdb -i refseq_genomic.tar.gz -title ref_data -out ref_data


          Someone any idea how it should be proceeded?

          Comment


          • #6
            These are pre-made blast index files. You can start using them right away after extracting them from the archive.


            Originally posted by Sheera View Post
            Thanks GenoMax!
            But I am not agree I am not at itagain.
            I downloaded refseq_genomic_tar.gz data file from ftp://ftp.ncbi.nlm.nih.gov/blast/db/ like this

            ./update_blastdb.pl ftp://ftp.ncbi.nlm.nih.gov/blast/db/ refseq_genomic*

            I gunzip and got like 8 files as:
            refseq_genomic.nhr
            refseq_genomic.nin
            refseq_genomic.nid
            refseq_genomic.nnd
            refseq_genomic.nog
            refseq_genomic.nsi n more.
            I want to make this as file as my local database for the further blast thing.
            I have new blast ie blast+ working

            Now for formatdb, its makeblastdb.

            I dont know how the downloaded file works here as I tried many ways.
            ./makeblastdb -i refseq_genomic.tar.gz -title ref_data -out ref_data


            Someone any idea how it should be proceeded?

            Comment

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