Unconfigured Ad

Collapse
X
 
  • Time
  • Show
Clear All
new posts
  • biocomputer
    Member
    • Dec 2013
    • 62

    #1

    Repeats named with trailing underscore eg. ID4 vs ID4_, tRNA-Gln-CAA vs tRNA-Gln-CAA_

    I'm looking for repeats in my mouse ChIP-seq data using RepBase and RepeatMasker. I've downloaded the repeat information and found some repeats with the same names except one version has a trailing underscore and one does not. In RepBase a bunch of the tRNA repeats are like this, the two versions having different consensus sequences, for example:

    Code:
    >tRNA-Gln-CAA	tRNA	Vertebrata
    ggtcccatggtgtaatggttagcactctggactttgaatccagcaatccgagttcgaatctcggtgggac
    ctcca
    >tRNA-Gln-CAA_	tRNA	Vertebrata
    taggacatggtgtaataggtagcacggagaattttgaattctcaggggtaggttcaattcctatagttct
    Another example, RepeatMasker has both ID4 and ID4_ while RepBase has just ID4_.

    Do these underscores mean something specific or are they just repeats that are similar so whoever was in charge of naming them just decided to name them like this?
  • SES
    Senior Member
    • Mar 2010
    • 275

    #2
    The best way to find out for certain would be to email the people at RepBase and ask because it does not appear to be documented on their website, and it isn't clear from the annotation files. I would be very interested to know what this means, so please post the answer if you find out what the trailing underscore indicates.

    Comment

    Latest Articles

    Collapse

    • SEQadmin2
      16S/ITS Profiling vs. Shotgun Metagenomics: What Changes in Your Workflow?
      by SEQadmin2




      NGS has revolutionized clinical microbiology by offering new ways to identify and surveil pathogens without prior knowledge of the target. One popular approach is 16S rRNA and ITS amplicon sequencing, which targets specific microbial markers. But studies are increasingly incorporating shotgun metagenomics, a technique that sequences all DNA from a sample without targeting specific microbial markers. This approach allows more detailed taxonomic classification, detection...
      Today, 06:46 AM
    • 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

    ad_right_rmr

    Collapse

    News

    Collapse

    Topics Statistics Last Post
    Started by SEQadmin2, 10-28-2026, 09:57 AM
    0 responses
    24 views
    0 reactions
    Last Post SEQadmin2  
    Started by SEQadmin2, 10-28-2026, 09:51 AM
    0 responses
    15 views
    0 reactions
    Last Post SEQadmin2  
    Started by SEQadmin2, 10-22-2026, 11:13 AM
    0 responses
    70 views
    0 reactions
    Last Post SEQadmin2  
    Started by SEQadmin2, 10-22-2026, 10:48 AM
    0 responses
    48 views
    0 reactions
    Last Post SEQadmin2  
    Working...