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  • dna, dna_sm and dna_rm which one should I use to form a blast database?

    I saw there are a couple of files on the ensembl ftp website:

    ftp://ftp.ensembl.org/pub/release-76...lanoleuca/dna/

    * 'dna' - unmasked genomic DNA sequences.

    * 'dna_rm' - masked genomic DNA. Interspersed repeats and low
    complexity regions are detected with the RepeatMasker tool and masked
    by replacing repeats with 'N's.

    * 'dna_sm' - soft-masked genomic DNA. All repeats and low complexity regions
    have been replaced with lowercased versions of their nucleic base

    Still don't know which file should I downloaded to format a blast database? Thanks!

  • #2
    What are you going to do using the blast database you create?

    Comment


    • #3
      Originally posted by GenoMax View Post
      What are you going to do using the blast database you create?
      Just normal blast, might want to know which species belongs to for those samples I already sequenced.

      Thanks for your reply.

      Comment


      • #4
        Get the unmasked DNA for a normal blast.

        Comment

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