Class HgvsDna


  • public class HgvsDna
    extends Hgvs
    Coding DNA reference sequence References http://www.hgvs.org/mutnomen/recs.html Nucleotide numbering: - there is no nucleotide 0 - nucleotide 1 is the A of the ATG-translation initiation codon - the nucleotide 5' of the ATG-translation initiation codon is -1, the previous -2, etc. - the nucleotide 3' of the translation stop codon is *1, the next *2, etc. - intronic nucleotides (coding DNA reference sequence only) - beginning of the intron; the number of the last nucleotide of the preceding exon, a plus sign and the position in the intron, like c.77+1G, c.77+2T, .... - end of the intron; the number of the first nucleotide of the following exon, a minus sign and the position upstream in the intron, like ..., c.78-2A, c.78-1G. - in the middle of the intron, numbering changes from "c.77+.." to "c.78-.."; for introns with an uneven number of nucleotides the central nucleotide is the last described with a "+" (see Discussion) Genomic reference sequence - nucleotide numbering starts with 1 at the first nucleotide of the sequence NOTE: the sequence should include all nucleotides covering the sequence (gene) of interest and should start well 5' of the promoter of a gene - no +, - or other signs are used - when the complete genomic sequence is not known, a coding DNA reference sequence should be used - for all descriptions the most 3' position possible is arbitrarily assigned to have been changed (see Exception)
    • Method Summary

      All Methods Instance Methods Concrete Methods 
      Modifier and Type Method Description
      protected java.lang.String alt()  
      protected java.lang.String dnaBaseChange()
      DNA level base changes
      protected boolean isDuplication()
      Is this a duplication?
      protected java.lang.String pos()
      Genomic position for exonic variants
      protected java.lang.String pos​(int pos)
      HGVS position base on genomic coordinates (chr is assumed to be the same as in transcript/marker).
      protected java.lang.String posDownstream​(int pos)
      Position downstream of the transcript
      protected java.lang.String posExon​(int pos)
      Convert genomic position to HGVS compatible (DNA) position
      protected java.lang.String posIntron​(int pos, Intron intron)
      Intronic position
      protected java.lang.String posUpstream​(int pos)
      Position upstream of the transcript
      protected java.lang.String posUtr3​(int pos)
      Position within 3'UTR
      protected java.lang.String posUtr5​(int pos)
      Position within 5'UTR
      protected java.lang.String prefixTranslocation()
      Translocation nomenclature.
      protected java.lang.String ref()  
      java.lang.String toString()  
      protected java.lang.String typeOfReference()
      Prefix for coding or non-coding sequences
      • Methods inherited from class java.lang.Object

        clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait
    • Field Detail

      • debug

        public static boolean debug
    • Constructor Detail

    • Method Detail

      • alt

        protected java.lang.String alt()
      • dnaBaseChange

        protected java.lang.String dnaBaseChange()
        DNA level base changes
      • isDuplication

        protected boolean isDuplication()
        Is this a duplication?
      • pos

        protected java.lang.String pos()
        Genomic position for exonic variants
      • pos

        protected java.lang.String pos​(int pos)
        HGVS position base on genomic coordinates (chr is assumed to be the same as in transcript/marker).
      • posDownstream

        protected java.lang.String posDownstream​(int pos)
        Position downstream of the transcript
      • posExon

        protected java.lang.String posExon​(int pos)
        Convert genomic position to HGVS compatible (DNA) position
      • posIntron

        protected java.lang.String posIntron​(int pos,
                                             Intron intron)
        Intronic position
      • posUpstream

        protected java.lang.String posUpstream​(int pos)
        Position upstream of the transcript
      • posUtr3

        protected java.lang.String posUtr3​(int pos)
        Position within 3'UTR
      • posUtr5

        protected java.lang.String posUtr5​(int pos)
        Position within 5'UTR
      • prefixTranslocation

        protected java.lang.String prefixTranslocation()
        Translocation nomenclature. From HGVS: Translocations are described at the molecular level using the format "t(X;4)(p21.2;q34)", followed by the usual numbering, indicating the position translocation breakpoint. The sequences of the translocation breakpoints need to be submitted to a sequence database (Genbank, EMBL, DDJB) and the accession.version numbers should be given (see Discussion). E.g.: t(X;4)(p21.2;q35)(c.857+101_857+102) denotes a translocation breakpoint in the intron between coding DNA nucleotides 857+101 and 857+102, joining chromosome bands Xp21.2 and 4q34
      • ref

        protected java.lang.String ref()
      • toString

        public java.lang.String toString()
        Overrides:
        toString in class java.lang.Object
      • typeOfReference

        protected java.lang.String typeOfReference()
        Prefix for coding or non-coding sequences