Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • Standalone BLAST results

    Hi,

    I used to standalone BLAST to subtract the Clostridium difficile proteome from the human proteome, using the command
    >blastp -db Human -in Mybacteria.fas -out results.fas -evalue 1e-3 -outfmt 4
    The results showed the query hits where the Clostridiums proteome matched the humans, I now need to subtract these matched sequences from the whole clostridium proteome and wondered if there was a quicker efficient way of doing this.
    Also if there was is a website that showed how to analyse the results.

    Many thanks,

    Dani

  • #2
    You probably need to write a script to do this. Biopython might be a good place to look at for an easy way to parse fasta files.

    Comment


    • #3
      if you output your blast results in tabular format then you could try the following.

      In terminal try the following:

      Code:
      grep -w Clostridiums input_file > output_file1
      
      grep -w proteome output_file1 > final_output_file
      Hope this help.

      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, 03-27-2024, 06:37 PM
      0 responses
      13 views
      0 likes
      Last Post seqadmin  
      Started by seqadmin, 03-27-2024, 06:07 PM
      0 responses
      11 views
      0 likes
      Last Post seqadmin  
      Started by seqadmin, 03-22-2024, 10:03 AM
      0 responses
      53 views
      0 likes
      Last Post seqadmin  
      Started by seqadmin, 03-21-2024, 07:32 AM
      0 responses
      69 views
      0 likes
      Last Post seqadmin  
      Working...
      X