Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • Terminology question from a novice

    Hi all,

    My lab has recently started using 454 GS FLX titanium pyroseqeuncing of cDNAs for several transcriptome projects with non-model organisms. All of our data has been assembled by Newbler 2.3 and later annotated by search against BLASTx nr database.

    We are debating how we should refer to the assembled "isogroups" in our paper. Is appropriate to refer to an "isogroup" as a gene? Or a 'gene'? What about a isotigs or contigs that are not assembled into isogroups but are annotated?

    Thanks for you help!

  • #2
    As an aside, why are you not using Newbler 2.5? Reportedly it does a better job, see e.g.
    Kumar and Blaxter (2010), http://www.biomedcentral.com/1471-2164/11/571

    Comment


    • #3
      I guess the best thing would be to annotate all sequences and cluster them into gene families (or this in reverse order) before calling any two different sequences two different genes or 'genes'...

      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
      10 views
      0 likes
      Last Post seqadmin  
      Started by seqadmin, Yesterday, 06:07 PM
      0 responses
      9 views
      0 likes
      Last Post seqadmin  
      Started by seqadmin, 03-22-2024, 10:03 AM
      0 responses
      50 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