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  • Standalone BLAST output

    Hello All,

    I'm using NCBI's standalone BLAST to annotate mRNA sequences from 454 sequencing.

    I'm using the "-outfmt 6" command as I like the table format, but I can't get the protein description to appear in one of the columns.

    The commands for specifically configuring the table output don't seem to have any options other than displaying the subject id or accession number..

    Any help would be greatly appreciated!

    Cheers,

    Matt.

  • #2
    I've not tried this, but there are some title options when creating the BLAST database which will influence what you can get in the output.

    Comment


    • #3
      Hello I am using a standalone CLC version 7.0.4 to do blast.
      I downloaded database files from ftp://ftp.ncbi.nlm.nih.gov/refseq/release/viral/.
      However, the results are weird to me i.e they do not give the identities or descriptions of the hits. Can someone help?

      Kaps

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      • #4
        Which output format are you using? With tabular you can ask for the BLAST hit descriptions (although if and how you do that via CLC I don't know). See e.g.
        This is an open letter to the NCBI BLAST+ team to request two simple enhancements which I think would be extremely useful - first and foremo...

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        • #5
          @kaps: Please email CLC tech support (http://www.clcbio.com/support/contact/) since you are likely to get a quicker answer from them than folks on the forum.

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          • #6
            hello maubp,

            I am not sure if CLC gives options for output format since i have not seen them!
            I will check the link you suggested.
            I have also tried commandline BLASTN 2.2.29+ but the results have no column headers, is this the usual format?

            Comment


            • #7
              Hello GenoMax,

              I will contact clc as suggested.

              thanks

              Comment


              • #8
                Originally posted by kaps View Post
                hello maubp,

                I am not sure if CLC gives options for output format since i have not seen them!
                As suggested above, ask CLC about that.
                Originally posted by kaps View Post
                I will check the link you suggested.
                I have also tried commandline BLASTN 2.2.29+ but the results have no column headers, is this the usual format?
                I wrote another blog post about the column headers too,
                In the last couple of years, my preferred BLAST output format has switched from BLAST XML to plain tabular output. The main reason for this ...

                Comment


                • #9
                  Hello Maubp, thanks for the blog posts, they were very helpful in generating column headers

                  kaps

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