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  • rdu
    Member
    • Aug 2010
    • 29
    #1

    question on making BLAST db

    Hi,

    I'm trying to make a BLAST database. The fasta file was downloaded from ftp://ftp.theseed.org/genomes/SEED/SEED.fasta.gz. Then I used commond line: makeblastdb -in seed.fasta -out seeddb -dbtype prot. But it shows a error message "Eror: Unable to open input seed.fasta as either FASTA file or BLAST db".

    The seed.fasta is around 1.2G big. I opened it, the lines are like:

    >fig|100226.1.rna.129 unknown function
    ......................................................
    ......................................................

    >fig|100226.1.peg.6568 putative membrane protein (GT:3483031)
    MKQGKEVENPESRFFAVLLAAA..................................................
    ........................................................................................
    ......................................LGRDFSNTSFAAAPAPPAEPGPETPTVRG


    What cause the error? Thanks in advance.
    Tags: None
  • dschika
    Member
    • Mar 2010
    • 56
    #2
    First of all: Have you renamed the 'SEED.fasta' to 'seed.fasta'?
    Furthermore, it looks like your fasta file isn't complete valid. At the beginning of the file there are some fasta entries without sequence. You could delete them and try again!

    Comment

    • anna_
      Member
      • Dec 2010
      • 15
      #3
      Try to use "-hash_index" in your command. I don't exactly the reason, but I think this causes a kind referencing your database file.

      anna

      Comment

      • rdu
        Member
        • Aug 2010
        • 29
        #4
        Appreciate, dschika and anna.

        The mistake I made is I wasn't at the correct directory. After I switched there "makeblastdb" did take actions. But just like what you both pointed out, the "SEED.fasta" isn't completely valid. (Error message showed as Bad Char String some things.)

        My question is seems it isn't applicable to manually edit the big size .fasta file (1.2G), because even just a simple click on the file would take some time to response. Any better way to work on fasta file?

        I haven't had a chance to try "-hash_index", but I checked the BLAST maual. It works for "Enables the creation of sequence hash values. These hash values can then
        be used to quickly determine if a given sequence data exists in this BLAST database." I'm confused, because I haven't had a database by this point.

        By the way, something interrupted and made me reply so late, sorry!

        Comment

        • dschika
          Member
          • Mar 2010
          • 56
          #5
          I don't know your programmig skills, but I would write a small python or perl script.

          Comment

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