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  • SDPA_Pet
    Senior Member
    • Apr 2013
    • 222
    #1

    RDP database

    Can I download RDP database from NCBI? There are some database on NCBI ftp (e.g.16SMicrobial.tar.gz, refseq_rna.00.tar.gz). Are these NCBI own database or they are from other sources (just in NCBI format)

    I try to download RDP database from here (http://rdp.cme.msu.edu/misc/resources.jsp)

    However, after I download it, I am not sure which format (or database) I should use.

    I want to use BLASTn to blast my sequences data and my data are not aligned. Should I use Unaligned database from the website?

    Also, should I use "Genbank, unaligned". What does Genebank mean on the website? Does it mean RDP_10_32 database in genebank format? or It means the NCBI rRNA database. Can I use it directly for blastn command? or I need to convert the database to NCBI request database.

    Best regards,
    Ben
    Tags: None
    • GenoMax
      Senior Member
      • Feb 2008
      • 7142
      #2
      Originally posted by SDPA_Pet View Post

      I try to download RDP database from here (http://rdp.cme.msu.edu/misc/resources.jsp)

      However, after I download it, I am not sure which format (or database) I should use.

      I want to use BLASTn to blast my sequences data and my data are not aligned. Should I use Unaligned database from the website?

      Also, should I use "Genbank, unaligned". What does Genebank mean on the website? Does it mean RDP_10_32 database in genebank format? or It means the NCBI rRNA database. Can I use it directly for blastn command? or I need to convert the database to NCBI request database.

      Best regards,
      Ben
      If you start with the release10_32_unaligned.fa FASTA format file you will have to create a blast database from it. You can't directly use it for blastn. Instructions on how to create a blastable database from a fasta (makeblastdb) file are available at the blast command line help page: http://www.ncbi.nlm.nih.gov/books/NBK1763/

      release10_32_unaligned.gb appears to have the same sequences in GenBank format.

        Comment

        • SDPA_Pet
          Senior Member
          • Apr 2013
          • 222
          #3
          Originally posted by GenoMax View Post
          If you start with the release10_32_unaligned.fa FASTA format file you will have to create a blast database from it. You can't directly use it for blastn. Instructions on how to create a blastable database from a fasta (makeblastdb) file are available at the blast command line help page: http://www.ncbi.nlm.nih.gov/books/NBK1763/

          release10_32_unaligned.gb appears to have the same sequences in GenBank format.
          What are those aligned databases for? Are they better for blast?

            Comment

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