Package org.snpeff.codons
Class CodonTable
java.lang.Object
org.snpeff.codons.CodonTable
A codon translation table
- Author:
- pcingola
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Field Summary
Fields -
Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionTranslate codons to an amino acid sequenceaaThreeLetterCode
(char aa) Convert 1-letter code to 3-letter code (amino acids) Reference: http://www.hgvs.org/mutnomen/standards.html#aalistTranslate an amino acid into a codonint
degenerate
(String codon, int pos) Degree of "degenerate site" What is a "degenerate site"? Here is an explanation form Stephen Wright (Univ.getName()
boolean
Is 'codon' a start codon in this table?boolean
isStartFirst
(String codon) Is the first codon a 'start' codon?boolean
Is 'codon' a stop codon in this table?boolean
Is there a stop codon in this amino acid sequenceboolean
isStopAaSymbol
(char aaSymbol) toString()
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Field Details
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TERMINATION_CODON
- See Also:
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TERMINATION_CODON_1
- See Also:
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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:
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Constructor Details
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CodonTable
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Method Details
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aa
Translate codons to an amino acid sequence -
aa
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aaThreeLetterCode
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aaThreeLetterCode
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
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codon
Translate an amino acid into a codon -
degenerate
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
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getName
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isStart
Is 'codon' a start codon in this table? -
isStartFirst
Is the first codon a 'start' codon? -
isStopAaSymbol
public boolean isStopAaSymbol(char aaSymbol) -
isStop
Is 'codon' a stop codon in this table? -
isStopAa
Is there a stop codon in this amino acid sequence -
toString
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