Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • Creating a Command Line BLAST+ Database

    Hey guys,

    I am relatively new to linux and command line and have a basic understanding of the basic commands in regards to the terminal.

    What I want to do is set up local BLAST+ databases so I can BLAST hundreds of sequences against the blastx or blastn databases.

    So far I have downloaded the latest databases, extracted them via gunzip, and copied them into my usr/local/bin folder. I believe this allows me to run BLAST applications from anywhere.

    I do not know where to go next. Do I have to format the blastx and blastn databases before I can blast my sequences? If so can any of you please point me in the right direction in how to do this?

    Any help is appreciated, thank you very much!

    Ryan.

  • #2
    As long as you downloaded the pre-formatted databases from (ftp://ftp.ncbi.nlm.nih.gov/blast/db/) you can use them directly with blast+. You have also got the executables for your OS: ftp://ftp.ncbi.nlm.nih.gov/blast/exe...last+/LATEST/?

    Follow the command line manual for blast to start your analysis: http://www.ncbi.nlm.nih.gov/books/NBK1763/

    Keep realistic expectations if you are going to do the blast locally, specially if you have modest hardware (post specs if you need any specific comments on that). It will take time to blastx several hundred sequences against nr.

    Comment


    • #3
      Hello GenoMax,

      Thanks for the help. To begin I have downloaded the pre-formatted nt database.

      Once I unzip all the files associated with the nt database do I place them in the same directory as I have placed the BLAST+ executables? Once this is done I assume I will be able to run a search using one of my fasta files against the nt database.

      Thank you,

      Ryan.

      Comment


      • #4
        Originally posted by GSviral View Post
        Hello GenoMax,

        Thanks for the help. To begin I have downloaded the pre-formatted nt database.

        Once I unzip all the files associated with the nt database do I place them in the same directory as I have placed the BLAST+ executables? Once this is done I assume I will be able to run a search using one of my fasta files against the nt database.

        Thank you,

        Ryan.
        You can put the database files where ever convenient. When you start your blast you will specify DB location by using the -db command line option and providing the path to the files. All the pieces for a set (numerically named files) need to be in the same directory and you only need to use the base name i.e. nr (do not include the numbers)

        Comment

        Latest Articles

        Collapse

        • 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
        • seqadmin
          The Impact of AI in Genomic Medicine
          by seqadmin



          Artificial intelligence (AI) has evolved from a futuristic vision to a mainstream technology, highlighted by the introduction of tools like OpenAI's ChatGPT and Google's Gemini. In recent years, AI has become increasingly integrated into the field of genomics. This integration has enabled new scientific discoveries while simultaneously raising important ethical questions1. Interviews with two researchers at the center of this intersection provide insightful perspectives into...
          02-26-2024, 02:07 PM

        ad_right_rmr

        Collapse

        News

        Collapse

        Topics Statistics Last Post
        Started by seqadmin, 03-14-2024, 06:13 AM
        0 responses
        34 views
        0 likes
        Last Post seqadmin  
        Started by seqadmin, 03-08-2024, 08:03 AM
        0 responses
        72 views
        0 likes
        Last Post seqadmin  
        Started by seqadmin, 03-07-2024, 08:13 AM
        0 responses
        82 views
        0 likes
        Last Post seqadmin  
        Started by seqadmin, 03-06-2024, 09:51 AM
        0 responses
        68 views
        0 likes
        Last Post seqadmin  
        Working...
        X