Unconfigured Ad

Collapse
X
 
  • Time
  • Show
Clear All
new posts
  • Applemelon
    Junior Member
    • Jun 2012
    • 4

    #1

    What is the specification of dbSNP?

    I downloaded from NCBI dbSNP a file, whose format is something like fasta. Here is one example:

    >gnl|dbSNP|ss244318098 ss=244318098|pos=394|len=894|handle="BGI"|subid="Gm01-394"|taxid=3847|mol="Genomic"|class=1|alleles="A/C"
    GGTTTGGTGTTTGGGTTTTAGGTTTTAGGTTTTAGGTTTTACGGTTTAGGGTTTATGGTTTATGGTTTAGGGTTTAGGGT
    TAGGAAATAATTTGGGTCTTTCATCTTTCAACAAAAAATTAAGGGATTTAGAGTAATTTTTAGGGTTTAGGGTTTAAGGT
    TTTAGGTTTCGGGTTTGGGTTTTAGATTTTACGGCTTACGGTTTAAAGTTTAGGGGTTAGGGTTTAGGGTTTAGAAATAA
    ATTTGAGTGTTTGACATTTGAACACAAAATTAAGGCATTTAGAGTCATTTTTAGGGTTTACGGTTTAGGGTTTAGCAAGA
    AATTTCGGTGTTTCATCTTCGAACACAAAATTAAGGCAGTTAAAGTCTTTTTTTGGGTTTAGGGTTTAGGGTT
    M
    TTTGCCTGGGTGTGCCAGTGGCGTGAGCAAATGGAGGGCGGCCATTTCTCATGTTTGGACGTCAAAGAACCCATAAAAAA
    TAGTCCTGTTCCCCGGTTTCGTCAACTAACACGTAAAAACAATGCCTTAACACAAAATTAAGGCATTTAGAGGCATTTTT
    AGGGTTTACGGTTTAGGGTTTACCAAGAAATTTCGGTGTTTCATCTTTGAACACAAAATTAAGGCAGTTAAAGTCTTTTT

    I was confused by "class=1“ in the header and "M" in the body. What are their meanings? How to transfer this format to VCF format? I can't find VCF file of soybean. Thank you very much.
  • ulz_peter
    Senior Member
    • Feb 2010
    • 219

    #2
    The lonesome "M" in the middle of the text is IUPAC Ambiguity Code. This is used if you want to state that two or more bases are likely to be in the same position. In this case the letter M is short for aMino, which means there can be either C or A at that position.

    I don't think it is possible to generate a VCF file from just having this position, since it neither states a chromsome nor a position for that SNP, which is necessary for creating a VCF.

    If you've got a lot of time you might align those seuqences and then annotate the missing infomration to get a VCF file, but there might be easier solutions for that

    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
    22 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
    68 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...