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  • All agains All BLAST

    Hello,

    I need a tool that can blast proteins sequences in a multifasta file against each other. I mean if there are 10 proteins, I need to blast each one of the ten with the other 9, and reports significant hits.
    I used before avaBLAST, but now I can't find the download files.

    Thanks,

  • #2
    Blat can do this easily: http://users.soe.ucsc.edu/~kent/src/
    You will need to decide on a output format that suits your purpose and perhaps do some scripting to fish out results you need.

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    • #3
      blastall does this

      Comment


      • #4
        Originally posted by bioBob View Post
        blastall does this
        Hello

        Thanks for the reply..
        I typed the following command:
        makeblastdb -in good_proteins.fasta -dbtype prot -out my_prot_blast_db

        But I can't find the output. can u please how can I retrieve the output?

        Thanks,

        Comment


        • #5
          all you have accomplished with that command is to format the db, now you need to actually do the blastall, here is what I use for the older blastall

          formatdb -i good_proteins.fasta -p T
          blastall -i good_proteins.fasta -d good_proteins.fasta -o results -m 8

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