Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • Minimal overlap between two reads in the de Bruijn algorithm

    I was reading a paper named "Comparison of the two major classes of assembly algorithms: overlap–layout–consensus and de-bruijn-graph" by Zhenyu Li et al. (2011), when I came across the following sentence:

    In the DBG algorithm, to ensure the k-mers can be linked, the minimum overlap between two reads should be no less than the k-mer size K that is equivalent to the T parameter in the Lander–Waterman model.
    I thought that the minimum overlap between two reads should be no less than K-1 and not K. I would really appreciate it if someone could explain me the quoted statement.

  • #2
    Originally posted by TauOvermind View Post
    I thought that the minimum overlap between two reads should be no less than K-1 and not K. I would really appreciate it if someone could explain me the quoted statement.
    Yes, you're right. In practice there's so little difference between K and K-1 that it's easy to make a mistake like that and overlook it.

    Comment


    • #3
      Thank you, Brian. I agree that the difference between these two values would be minimal in practice, but as it was a paper about the theory of sequence assembly, I found that statement confusing, as I thought that I might have been missing an important point in the derivation.
      Last edited by TauOvermind; 11-17-2015, 11:55 AM.

      Comment

      Latest Articles

      Collapse

      • seqadmin
        Current Approaches to Protein Sequencing
        by seqadmin


        Proteins are often described as the workhorses of the cell, and identifying their sequences is key to understanding their role in biological processes and disease. Currently, the most common technique used to determine protein sequences is mass spectrometry. While still a valuable tool, mass spectrometry faces several limitations and requires a highly experienced scientist familiar with the equipment to operate it. Additionally, other proteomic methods, like affinity assays, are constrained...
        04-04-2024, 04:25 PM
      • 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

      ad_right_rmr

      Collapse

      News

      Collapse

      Topics Statistics Last Post
      Started by seqadmin, 04-11-2024, 12:08 PM
      0 responses
      31 views
      0 likes
      Last Post seqadmin  
      Started by seqadmin, 04-10-2024, 10:19 PM
      0 responses
      32 views
      0 likes
      Last Post seqadmin  
      Started by seqadmin, 04-10-2024, 09:21 AM
      0 responses
      28 views
      0 likes
      Last Post seqadmin  
      Started by seqadmin, 04-04-2024, 09:00 AM
      0 responses
      53 views
      0 likes
      Last Post seqadmin  
      Working...
      X