Package org.snpeff.interval
Class RareAminoAcid
- java.lang.Object
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- org.snpeff.interval.Interval
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- org.snpeff.interval.Marker
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- org.snpeff.interval.RareAminoAcid
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- All Implemented Interfaces:
java.io.Serializable
,java.lang.Cloneable
,java.lang.Comparable<Interval>
,TxtSerializable
public class RareAminoAcid extends Marker
Rare amino acid annotation: These are amino acids that occurs very rarely in an organism. For instance, humans are supposed to use 20 amino acids, but there is also one rare AA. Selenocysteine, single letter code 'U', appears roughly 100 times in the whole genome. The amino acid is so rare that usually it does not appear in codon translation tables. It is encoded as UGA, which , under normal conditions, is a STOP codon. Secondary RNA structures are assumed to enable this special translation.- Author:
- pcingola
- See Also:
- Serialized Form
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Field Summary
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Fields inherited from class org.snpeff.interval.Interval
chromosomeNameOri, end, id, parent, start, strandMinus
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Constructor Summary
Constructors Constructor Description RareAminoAcid()
RareAminoAcid(Marker parent, int start, int end, java.lang.String id)
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Method Summary
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Methods inherited from class org.snpeff.interval.Marker
adjust, apply, applyDel, applyDup, applyIns, applyMixed, clone, cloneShallow, codonTable, compareTo, compareToPos, distance, distanceBases, getParent, getType, idChain, idChain, idChain, includes, intersect, isAdjustIfParentDoesNotInclude, isShowWarningIfParentDoesNotInclude, minus, query, query, readTxt, serializeParse, serializeSave, shouldApply, toString, union, variantEffect, variantEffectNonRef
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Methods inherited from class org.snpeff.interval.Interval
equals, findParent, getChromosome, getChromosomeName, getChromosomeNameOri, getChromosomeNum, getEnd, getGenome, getGenomeName, getId, getStart, getStrand, hashCode, intersects, intersects, intersects, intersects, intersectSize, isCircular, isSameChromo, isStrandMinus, isStrandPlus, isValid, setChromosomeNameOri, setEnd, setId, setParent, setStart, setStrandMinus, shiftCoordinates, size, toStr, toStringAsciiArt
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Constructor Detail
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RareAminoAcid
public RareAminoAcid()
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RareAminoAcid
public RareAminoAcid(Marker parent, int start, int end, java.lang.String id)
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