Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • Standalone blast

    Hi

    I have downloaded standalone blast and formatted a nucleotide database. I wish to use tblastn to compare Arabidopsis proteins against it. I made a db folder in the folder where blast is saved and changed to that directory then ran the following command:

    tblastn -query tair1prot -db petunia -evalue 0.01

    However I receive an error:

    BLAST Database error: No alias or index file found for the nucleotide database [petunia] in search path [C:\Program Files\NCBI\blast-2.2.25+\db;C:\Program Files\NCBI\blast-2.2.25+\db;]

    As you can see I think the program is taking the file path of the current directory and then adding the directory where databases are stored on to the end. This would mean the db directory and the index file are not found. If I change directory to C:\ for instance then the errror would be C:\;C:\Program Files\NCBI\blast-2.2.25+\db;

    How can I stop this from happening so the database can be located correctly? What do you think I might be doing wrong?

    Thanks

    Jon

  • #2
    The simplest answers are either tell BLAST where you files are (instead of -db petunia use something like -db "C:\my files\petunia"), or put your files in the BLAST database folder where BLAST automatically looks, C:\Program Files\NCBI\blast-2.2.25+\db

    Comment


    • #3
      did you format your database? I get the same error when I forget to run formatdb

      Comment


      • #4
        Hi

        Thanks for your replies.

        I was using makeblastdb which I think formats the db so I think my problem was a permissions issue. I ran tblastn from a folder in my documents and the output file was created there (it wouldn't work when running from within program files).

        I've had success running one or two proteins against the nucleotide database. However, now I've started the program with the entire TAIR protein database it is understandably taking a long time to run. My nucleotide database is about 1.3MB in length and I believe there are ~300000 proteins. How long can I expect this to take on a normal pc (i7 processor/4GB RAM) or should I really be thinking about running it on a supercomputer?

        Thanks

        Jon

        Comment

        Latest Articles

        Collapse

        • seqadmin
          Best Practices for Single-Cell Sequencing Analysis
          by seqadmin



          While isolating and preparing single cells for sequencing was historically the bottleneck, recent technological advancements have shifted the challenge to data analysis. This highlights the rapidly evolving nature of single-cell sequencing. The inherent complexity of single-cell analysis has intensified with the surge in data volume and the incorporation of diverse and more complex datasets. This article explores the challenges in analysis, examines common pitfalls, offers...
          06-06-2024, 07:15 AM
        • seqadmin
          Latest Developments in Precision Medicine
          by seqadmin



          Technological advances have led to drastic improvements in the field of precision medicine, enabling more personalized approaches to treatment. This article explores four leading groups that are overcoming many of the challenges of genomic profiling and precision medicine through their innovative platforms and technologies.

          Somatic Genomics
          “We have such a tremendous amount of genetic diversity that exists within each of us, and not just between us as individuals,”...
          05-24-2024, 01:16 PM

        ad_right_rmr

        Collapse

        News

        Collapse

        Topics Statistics Last Post
        Started by seqadmin, 06-07-2024, 06:58 AM
        0 responses
        179 views
        0 likes
        Last Post seqadmin  
        Started by seqadmin, 06-06-2024, 08:18 AM
        0 responses
        228 views
        0 likes
        Last Post seqadmin  
        Started by seqadmin, 06-06-2024, 08:04 AM
        0 responses
        184 views
        0 likes
        Last Post seqadmin  
        Started by seqadmin, 06-03-2024, 06:55 AM
        0 responses
        18 views
        0 likes
        Last Post seqadmin  
        Working...
        X