Unconfigured Ad

Collapse
X
 
  • Time
  • Show
Clear All
new posts
  • Yangan
    Junior Member
    • Nov 2015
    • 2

    #1

    How to extract nucleotide sequeces from tblastx table

    Hi there,

    I am a new learner of bioinformatics.
    I used Trinity to do de novo transcriptome assembly then imported the assembly.fasta file into CLC genomeworkbench 7.0.3 to run tblastx using this assembly file as local database while using all P450 cDNA of Arabidopsis as queries. Next step I would like to map reads to these contigs with hits. However, I don't know how to seive all the contigs with hits (nucleotide sequences) out after using tblastx since all sequences were translated in to amino acid sequences.
    I tried "Toolbox-Classical Sequence Analysis-General Sequence Analysis-Extract sequence", but only amino acid sequences were obtained. I could also extract the nucleotide sequence of a single contig every time, but there are thousands of contigs with hits in my case.
    Anyone knows how to achieve that?
  • GenoMax
    Senior Member
    • Feb 2008
    • 7142

    #2
    @Yangan: Since your CLC license includes free tech support you may want to contact them about this question (I assume you want to do this within CLC). They may need to provide you with a plugin or custom code to do the action you are referring to.

    Comment

    • Yangan
      Junior Member
      • Nov 2015
      • 2

      #3
      Originally posted by GenoMax View Post
      @Yangan: Since your CLC license includes free tech support you may want to contact them about this question (I assume you want to do this within CLC). They may need to provide you with a plugin or custom code to do the action you are referring to.
      Thank you for your suggestion

      Comment

      Latest Articles

      Collapse

      • SEQadmin2
        Multiomic Liquid Biopsy: What DNA/RNA Panels Reveal That DNA Alone Can’t
        by SEQadmin2



        Tumors contain complex mixtures of cell populations that evolve in response to treatment and host-specific factors. Tissue biopsies provide only static snapshots of a tumor’s state. But what if we could follow that evolution over time using a minimally invasive technique?

        Liquid biopsies can detect tumor-derived material circulating in the bloodstream, providing a way to study treatment response, detect emerging resistance, and discover new biomarkers. Circulating
        ...
        10-14-2026, 09:55 AM
      • SEQadmin2
        New Genomics Technologies Take Aim at Long-Standing Limits
        by SEQadmin2


        Researchers using sequencing and genomics tools often have to make trade-offs. They can choose between speed or scale, short reads or long-range information, or targeted panels or a view of the whole transcriptome. New technologies that have been released this year are built to address those tough choices.

        We asked six companies the same four questions to learn about their latest products. The new technologies bring a lot to the table, including rethinking sequencing
        ...
        09-28-2026, 10:25 AM

      ad_right_rmr

      Collapse

      News

      Collapse

      Topics Statistics Last Post
      Started by SEQadmin2, 10-22-2026, 11:13 AM
      0 responses
      21 views
      0 reactions
      Last Post SEQadmin2  
      Started by SEQadmin2, 10-22-2026, 10:48 AM
      0 responses
      18 views
      0 reactions
      Last Post SEQadmin2  
      Started by SEQadmin2, 10-15-2026, 10:52 AM
      0 responses
      36 views
      0 reactions
      Last Post SEQadmin2  
      Started by SEQadmin2, 10-14-2026, 05:39 AM
      0 responses
      42 views
      0 reactions
      Last Post SEQadmin2  
      Working...