Class CodonTable

java.lang.Object
org.snpeff.codons.CodonTable

public class CodonTable extends Object
A codon translation table
Author:
pcingola
  • Field Details

    • TERMINATION_CODON

      public static final String TERMINATION_CODON
      See Also:
    • TERMINATION_CODON_1

      public static final String TERMINATION_CODON_1
      See Also:
    • DEFAULT_START_CODON

      public static final String DEFAULT_START_CODON
      All start codons are translated as "M". Reference: https://en.wikipedia.org/wiki/Start_codon Alternative start codons are different from the standard AUG codon and are found in both prokaryotes (bacteria) and eukaryotes. Alternate start codons are still translated as Met when they are at the start of a protein (even if the codon encodes a different amino acid otherwise). This is because a separate transfer RNA (tRNA) is used for initiation.
      See Also:
  • Constructor Details

    • CodonTable

      public CodonTable(String name, String table)
  • Method Details

    • aa

      public String aa(String codons)
      Translate codons to an amino acid sequence
    • aa

      public String aa(String codons, boolean fullProteinSequence)
    • aaThreeLetterCode

      public String aaThreeLetterCode(char aa)
    • aaThreeLetterCode

      public String aaThreeLetterCode(String aa)
      Convert 1-letter code to 3-letter code (amino acids) Reference: http://www.hgvs.org/mutnomen/standards.html#aalist
      Parameters:
      Amino - acid in three letter code
    • codon

      public List<String> codon(String aa)
      Translate an amino acid into a codon
    • degenerate

      public int degenerate(String codon, int pos)
      Degree of "degenerate site" What is a "degenerate site"? Here is an explanation form Stephen Wright (Univ. Toronto), who requested to add this feature "...a fourfold degenerate site would be a site where any change is synonymous. So the third codon position for the arginine CGN, is a fourfold degenerate site, as is the third codon position for valine, alanine, etc. Similarly, all second positions of a codon are zerofold degenerate, since any change is nonsynonymous. Many first codon positions are also zerofold degenerate, however, for example, the first codon position of AGG is NOT zerofold, because a shift to CGG is a synonymous change."
      Parameters:
      codon -
      pos -
      Returns:
      Degenracy level, or '-1' if not available
    • getName

      public String getName()
    • isStart

      public boolean isStart(String codon)
      Is 'codon' a start codon in this table?
    • isStartFirst

      public boolean isStartFirst(String codon)
      Is the first codon a 'start' codon?
    • isStop

      public boolean isStop(String codon)
      Is 'codon' a stop codon in this table?
    • isStopAa

      public boolean isStopAa(String aas)
      Is there a stop codon in this amino acid sequence
    • toString

      public String toString()
      Overrides:
      toString in class Object