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  • Who let M's and R's in the Genome

    Just looking for other peoples input on something

    Has anyone notice there are two R and one M IUPAC codes on chromosome 3 in the reference genomes, both NCBI36 and GRCh37. Maybe not surprisingly they sit in the FHIT gene.

    Does this worry anyone for genome indexing or the such, seems minor in 3/3billion.
    Attached Files

  • #2
    Yes I noticed that, they are quite odd... I just replace them with N's when doing analysis.
    SpliceMap: De novo detection of splice junctions from RNA-seq
    Download SpliceMap Comment here

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    • #3
      Surprisingly, I noticed this yesterday too!
      Not expected, but no clue if it affects things downstream...
      --
      bioinfosm

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      • #4
        I know in some cases they use N to mask sequence that are repeats.

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        • #5
          the other letters in the code

          m= a or c, as in amino

          r= g or a, as in purine

          n= a or g or c or t/u, unknown, or other

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          • #6
            Originally posted by Joann View Post
            m= a or c, as in amino

            r= g or a, as in purine

            n= a or g or c or t/u, unknown, or other
            ah ha, good to know, thanks!

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            • #7
              Wait! there's more...

              Please see Annex C, Appendix 2, Table 1, page 16 at, for example,

              http://www.noip.gov.vn/noip/resource.nsf/vwResourceList/B4F5E35FA26A8AA4472577360013F1D3/$FILE/Standards%20%E2%80%93%20ST25.pdf

              for a complete list of nucleotide letter symbols in use per a current international standard.

              See also
              An extended IUPAC nomenclature code for polymorphic
              nucleic acids
              doi:10.1093/bioinformatics/btq098
              Last edited by Joann; 01-21-2011, 02:09 PM. Reason: update

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              • #8
                Interesting to know something apart from A,T,G,C,N.

                But UCSC has them as "N"s

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                • #9
                  These additional letters are sometimes called 'ambiguiety codes'. Back in the day when a 30X human genome sequence cost a billion dollars instead of several thousand, every piece of sequence information was much more precious. Knowing a position was a purine was better than calling it an N. The codes are also useful for reporting heterozygous genotype information as a single letter. The fact that they still occur in reference genomes is mostly just a nuisance for bioinformatics and thus some resources such as UCSC convert them to N's. I believe human genome sequences retrieved via Ensembl may still contain them though.

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