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  • gene coder
    replied
    Thanks. That is what I needed to know.

    Leave a comment:


  • Sacha Rybalka
    replied
    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

    Leave a comment:


  • gene coder
    started a topic Nucleotides M and R in human reference no. 37

    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
    ...

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