Seqanswers Leaderboard Ad

Collapse

Announcement

Collapse
No announcement yet.
X
 
  • Filter
  • Time
  • Show
Clear All
new posts

  • install local blast

    I tried to install local blast on my Linux machine. However, I don't see blastn, nor blastx, not blastp. Why??

    commands:

    >wget ftp://ftp.ncbi.nih.gov/blast/executa...4-linux.tar.gz

    >tar zxvf blast-2.2.25-x64-linux.tar.gz

    up to this step, under the directory of blast-2.2.25/bin/, I see those files below

    -rwxr-xr-x 1 3755 5333 7202584 2011-01-30 09:32 bl2seq
    -rwxr-xr-x 1 3755 5333 7191857 2011-01-30 09:32 blastall
    -rwxr-xr-x 1 3755 5333 6511061 2011-01-30 09:32 blastclust
    -rwxr-xr-x 1 3755 5333 6758201 2011-01-30 09:32 blastpgp
    -rwxr-xr-x 1 3755 5333 6812336 2011-01-30 09:32 copymat
    -rwxr-xr-x 1 3755 5333 6490648 2011-01-30 09:32 fastacmd
    -rwxr-xr-x 1 3755 5333 6498981 2011-01-30 09:32 formatdb
    -rwxr-xr-x 1 3755 5333 6803192 2011-01-30 09:32 formatrpsdb
    -rwxr-xr-x 1 3755 5333 6503411 2011-01-30 09:32 impala
    -rwxr-xr-x 1 3755 5333 6494292 2011-01-30 09:32 makemat
    -rwxr-xr-x 1 3755 5333 7183659 2011-01-30 09:32 megablast
    -rwxr-xr-x 1 3755 5333 7169549 2011-01-30 09:32 rpsblast
    -rwxr-xr-x 1 3755 5333 6538067 2011-01-30 09:32 seedtop

  • #2
    I guess you are missing something.. the above 'fastacmd' and 'formatdb' are from older version of blast. 2.2.25 version is blast+ and you should see 'blastdbcmd' and 'makeblastdb' for fastacmd and formatdb. and you will find blastn and blastp under bin only. Try to install in a new location.

    Comment


    • #3
      You downloaded from the older format C toolkit BLAST. To get the newer, C++ toolkit BLAST+ suite you should use this URL:

      Code:
      ftp.ncbi.nih.gov/blast/executables/blast+/LATEST/ncbi-blast-2.2.25+-x64-linux.tar.gz
      (I wrapped it in CODE tags so the board software would not try to automagically create a link. Copy this link and paste in another window if you want to download.)
      Last edited by kmcarr; 08-26-2011, 12:42 PM. Reason: Explain code tags

      Comment


      • #4
        just run blastall you'll see all the options, these are the old blast programs, now it's called blast+ suit, as mentioned above.

        Comment


        • #5
          Hi,

          When downloading databases for local blast, I realized NCBI does not hold uniprot database in their site. Is it possible to download uniprot from uniprot.org and use it in blastx? Do I have to format it somehow or does blast recognize it as it is?

          Thanks for your help

          Dave

          Comment


          • #6
            Dave,

            You can download the uniprot fasta sequences from: http://www.uniprot.org/downloads

            You will need to format and create blast indexes before you can use uniprot to blast against. You can find the help manual for blast here: http://www.ncbi.nlm.nih.gov/books/NBK52636/


            Originally posted by dnusol View Post
            Hi,

            When downloading databases for local blast, I realized NCBI does not hold uniprot database in their site. Is it possible to download uniprot from uniprot.org and use it in blastx? Do I have to format it somehow or does blast recognize it as it is?

            Thanks for your help

            Dave

            Comment

            Latest Articles

            Collapse

            • seqadmin
              Strategies for Sequencing Challenging Samples
              by seqadmin


              Despite advancements in sequencing platforms and related sample preparation technologies, certain sample types continue to present significant challenges that can compromise sequencing results. Pedro Echave, Senior Manager of the Global Business Segment at Revvity, explained that the success of a sequencing experiment ultimately depends on the amount and integrity of the nucleic acid template (RNA or DNA) obtained from a sample. “The better the quality of the nucleic acid isolated...
              03-22-2024, 06:39 AM
            • seqadmin
              Techniques and Challenges in Conservation Genomics
              by seqadmin



              The field of conservation genomics centers on applying genomics technologies in support of conservation efforts and the preservation of biodiversity. This article features interviews with two researchers who showcase their innovative work and highlight the current state and future of conservation genomics.

              Avian Conservation
              Matthew DeSaix, a recent doctoral graduate from Kristen Ruegg’s lab at The University of Colorado, shared that most of his research...
              03-08-2024, 10:41 AM

            ad_right_rmr

            Collapse

            News

            Collapse

            Topics Statistics Last Post
            Started by seqadmin, Yesterday, 06:37 PM
            0 responses
            11 views
            0 likes
            Last Post seqadmin  
            Started by seqadmin, Yesterday, 06:07 PM
            0 responses
            10 views
            0 likes
            Last Post seqadmin  
            Started by seqadmin, 03-22-2024, 10:03 AM
            0 responses
            51 views
            0 likes
            Last Post seqadmin  
            Started by seqadmin, 03-21-2024, 07:32 AM
            0 responses
            67 views
            0 likes
            Last Post seqadmin  
            Working...
            X