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  • How can I write a bash command to blast local nt database?

    I have been reading this.

    I was able to write a basic query using blast n as follows:
    Code:
    blastn -db ~/programming/blastexample/db/tdb -query ~/programming/blastexample/db/even_tribolium.fasta
    It seems to me that I must replace tdb (I used makedb to create this) with the downloaded local nt database?

    However, I now downloaded nt into local database and I have the following questions:
    • How can I blast my fasta file against local nt blast database?
    • Are there options only to output the species name, contig, and E-value?
    • Where did my nt local blast database go? ha ha ha.



    Thanks for considering my question and your patience. I am very new to all of this.

  • #2
    Originally posted by hyates View Post
    I have been reading this.

    I was able to write a basic query using blast n as follows:
    Code:
    blastn -db ~/programming/blastexample/db/tdb -query ~/programming/blastexample/db/even_tribolium.fasta
    It seems to me that I must replace tdb (I used makedb to create this) with the downloaded local nt database?

    However, I now downloaded nt into local database and I have the following questions:
    • How can I blast my fasta file against local nt blast database?
    • Are there options only to output the species name, contig, and E-value?
    • Where did my nt local blast database go? ha ha ha.



    Thanks for considering my question and your patience. I am very new to all of this.
    Some questions for you:

    1. Did you download all pre-formatted nt.nn.tar.gz files from this link: ftp://ftp.ncbi.nlm.nih.gov/blast/db/ and unzip them in a single directory. Do not do anything else to the files. This database is pre-formatted.

    When using the database provide -db /path_to/nt (do not worry about file numbers).

    2. Output options for blast: http://www.ncbi.nlm.nih.gov/books/NB...BLAST_search_r
    If you don't like what you see there are custom parsers available to get just what you need.

    Comment


    • #3
      Originally posted by GenoMax View Post
      Some questions for you:

      1. Did you download all pre-formatted nt.nn.tar.gz files from this link: ftp://ftp.ncbi.nlm.nih.gov/blast/db/ and unzip them in a single directory. Do not do anything else to the files. This database is pre-formatted.

      When using the database provide -db /path_to/nt (do not worry about file numbers).

      2. Output options for blast: http://www.ncbi.nlm.nih.gov/books/NB...BLAST_search_r
      If you don't like what you see there are custom parsers available to get just what you need.
      • I ran ./update_blastdb.pl nt but I don't think I specified a directory. Oh no...
      • Thanks for the link to options. I am hopeful it has what I need since I am asking for basic fields.

      Comment


      • #4
        Originally posted by hyates View Post
        • I ran ./update_blastdb.pl nt but I don't think I specified a directory. Oh no...
        This would be a large download. So depending on bandwidth available it could take some time. Make sure you have enough space available on disk and do not do this via wi-fi

        Comment


        • #5
          Originally posted by GenoMax View Post
          This would be a large download. So depending on bandwidth available it could take some time. Make sure you have enough space available on disk and do not try this on wi-fi
          Thanks. I think I tried this before and put it in the directory with update_blastdb.pl, so I moved the files to a new directory. However, I am rerunning the command into a directory I wish for it to be in.

          So, in theory, this command should work with the local blast nt I download, right? In otherwords, blast my fasta file against the local nt database?
          Code:
          blastn -db ~/path/to/my/local/nt/db -query ~/path/to/this/fasta/even_tribolium.fasta
          Last edited by hyates; 03-05-2015, 10:25 AM.

          Comment


          • #6
            Originally posted by hyates View Post
            Thanks. I think I tried this before and put it in the directory with update_blastdb.pl, so I moved the files to a new directory. However, I am rerunning the command into a directory I wish for it to be in.

            So, in theory, this command should work with the local blast nt I download, right? In otherwords, blast my fasta file against the local nt database?
            Code:
            blastn -db ~/path/to/my/local/nt/db -query ~/path/to/this/fasta/even_tribolium.fasta
            You minimally want something like this, if you want click-able html output:
            Code:
            $ blastn –query ~/path/to/this/fasta/even_tribolium.fasta -db /path_to/nt -task blastn -html -out out.html

            Comment

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