Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • 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.

  • #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

    • seqadmin
      Essential Discoveries and Tools in Epitranscriptomics
      by seqadmin




      The field of epigenetics has traditionally concentrated more on DNA and how changes like methylation and phosphorylation of histones impact gene expression and regulation. However, our increased understanding of RNA modifications and their importance in cellular processes has led to a rise in epitranscriptomics research. “Epitranscriptomics brings together the concepts of epigenetics and gene expression,” explained Adrien Leger, PhD, Principal Research Scientist...
      04-22-2024, 07:01 AM
    • 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

    ad_right_rmr

    Collapse

    News

    Collapse

    Topics Statistics Last Post
    Started by seqadmin, Yesterday, 11:49 AM
    0 responses
    13 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, 04-24-2024, 08:47 AM
    0 responses
    16 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, 04-11-2024, 12:08 PM
    0 responses
    61 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, 04-10-2024, 10:19 PM
    0 responses
    60 views
    0 likes
    Last Post seqadmin  
    Working...
    X