Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • Nucleotides M and R in human reference no. 37

    A, C, G and T are "normal" nucleotides and N represents unknown nucleotides in repetitive sequences or SNPs. When checking the reference genome from 1KGP, I found these odd nucleotides: M and R. Does anybody know anything about that?

    Code:
    >>> ref_f = open("human_g1k_v37.fasta", "r")
    >>> 
    >>> cnt = 0
    >>> 
    >>> for i in ref_f:
    ...     cnt += 1
    ...     if i[0] == ">":
    ...             print i, 
    ...             continue
    ...     
    ...     n = i.count("A") + i.count("C") + i.count("G") + i.count("T") + i.count("N")
    ...     
    ...     if n < len(i) - 1:
    ...             print cnt, i
    yields

    Code:
    ...
    >3 dna:chromosome chromosome:GRCh37:3:1:198022430:1
    9221347 CGCTACATAGCTGMCTTATTATTCGTGGTCCCCTATGACCCCCTGATCATTTTCCCTGAG
    9221351 CCRRGCTTGGTTCTAACAATGAATTTAATAAGAATTGTATTTAATCAATGTTTAAATATA
    ...

  • #2
    Hi!
    I'm not working with Human genome, but is it not the IUPAC annotation for alternative bases (as S for Strong if G or C)? The wiki page here http://en.wikipedia.org/wiki/Nucleic_acid_notation

    Comment


    • #3
      Thanks. That is what I needed to know.

      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
      25 views
      0 likes
      Last Post seqadmin  
      Started by seqadmin, 04-10-2024, 10:19 PM
      0 responses
      28 views
      0 likes
      Last Post seqadmin  
      Started by seqadmin, 04-10-2024, 09:21 AM
      0 responses
      24 views
      0 likes
      Last Post seqadmin  
      Started by seqadmin, 04-04-2024, 09:00 AM
      0 responses
      52 views
      0 likes
      Last Post seqadmin  
      Working...
      X