Package org.biojava.bio.seq

Class RNATools

java.lang.Object

org.biojava.bio.seq.RNATools

public final class RNATools
extends Object

Useful functionality for processing DNA and RNA sequences.

Author:

Matthew Pocock, Keith James (docs), Thomas Down, Greg Cox, Mark Schreiber, David Huen (refactoring), gwaldon (update genetic code translation tables)

Method Summary

Modifier and Type	Method	Description
static AtomicSymbol	a()
static AtomicSymbol	c()
static Symbol	complement(Symbol sym)	Complement the symbol.
static SymbolList	complement(SymbolList list)	Retrieve a complement view of list.
static ReversibleTranslationTable	complementTable()	Get a translation table for complementing DNA symbols.
static SymbolList	createRNA(String rna)	Return a new RNA SymbolList for rna.
static Sequence	createRNASequence(String rna, String name)	Return a new RNA Sequence for rna.
static Symbol	forIndex(int index)	Return the symbol for an index - compatible with index.
static Symbol	forSymbol(char token)	Retrieve the symbol for a symbol.
static AtomicSymbol	g()
static FiniteAlphabet	getCodonAlphabet()	Gets the (RNA x RNA x RNA) Alphabet
static ManyToOneTranslationTable	getGeneticCode(int table_num)	Retrieve a TranslationTable by number.
static ManyToOneTranslationTable	getGeneticCode(String name)	Retrieve a TranslationTable by name.
static Set	getGeneticCodeNames()	Retrieve a Set containing the name of each genetic code.
static FiniteAlphabet	getRNA()	Return the RNA alphabet.
static int	index(Symbol sym)	Return an integer index for a symbol - compatible with forIndex.
static Symbol	n()
static SymbolList	reverseComplement(SymbolList list)	Retrieve a reverse-complement view of list.
static SymbolList	transcribe(SymbolList list)	Deprecated. The naming of this method is confusing and inconsistent use either DNATools.toRNA(SymbolList list) or DNATools.transcribeToRNA(SymbolList list) depending on the desired behaivour.
static ReversibleTranslationTable	transcriptionTable()	Get a translation table for converting DNA to RNA.
static SymbolList	translate(SymbolList syms)	Translate RNA into protein (with termination symbols).
static AtomicSymbol	u()

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Method Detail

a

public static AtomicSymbol a()

g

public static AtomicSymbol g()

c

public static AtomicSymbol c()

u

public static AtomicSymbol u()

n

public static Symbol n()

getRNA

public static FiniteAlphabet getRNA()

Return the RNA alphabet.

Returns:

a flyweight version of the RNA alphabet

getCodonAlphabet

public static FiniteAlphabet getCodonAlphabet()

Gets the (RNA x RNA x RNA) Alphabet

Returns:

a flyweight version of the (RNA x RNA x RNA) alphabet

createRNA

public static SymbolList createRNA(String rna)
                            throws IllegalSymbolException

Return a new RNA SymbolList for rna.

Parameters:

rna - a String to parse into RNA

Returns:

a SymbolList created form rna

Throws:

IllegalSymbolException - if rna contains any non-RNA characters

createRNASequence

public static Sequence createRNASequence(String rna,
                                         String name)
                                  throws IllegalSymbolException

Return a new RNA Sequence for rna.

Parameters:

rna - a String to parse into RNA

name - a String to use as the name

Returns:

a Sequence created form dna

Throws:

IllegalSymbolException - if rna contains any non-DNA characters

index

public static int index(Symbol sym)
                 throws IllegalSymbolException

Return an integer index for a symbol - compatible with forIndex.

The index for a symbol is stable across virtual machines & invocations.

Parameters:

sym - the Symbol to index

Returns:

the index for that symbol

Throws:

IllegalSymbolException - if sym is not a member of the DNA alphabet

forIndex

public static Symbol forIndex(int index)
                       throws IndexOutOfBoundsException

Return the symbol for an index - compatible with index.

The index for a symbol is stable accross virtual machines & invocations.

Parameters:

index - the index to look up

Returns:

the symbol at that index

Throws:

IndexOutOfBoundsException - if index is not between 0 and 3

complement

public static Symbol complement(Symbol sym)
                         throws IllegalSymbolException

Complement the symbol.

Parameters:

sym - the symbol to complement

Returns:

a Symbol that is the complement of sym

Throws:

IllegalSymbolException - if sym is not a member of the RNA alphabet

forSymbol

public static Symbol forSymbol(char token)
                        throws IllegalSymbolException

Retrieve the symbol for a symbol.

Parameters:

token - the char to look up

Returns:

the symbol for that char

Throws:

IllegalSymbolException - if the char is not a valid IUB code.

complement

public static SymbolList complement(SymbolList list)
                             throws IllegalAlphabetException

Retrieve a complement view of list.

Parameters:

list - the SymbolList to complement

Returns:

a SymbolList that is the complement

Throws:

IllegalAlphabetException - if list is not a complementable alphabet

reverseComplement

public static SymbolList reverseComplement(SymbolList list)
                                    throws IllegalAlphabetException

Retrieve a reverse-complement view of list.

Parameters:

list - the SymbolList to complement

Returns:

a SymbolList that is the complement

Throws:

IllegalAlphabetException - if list is not a complementable alphabet

transcribe

public static SymbolList transcribe(SymbolList list)
                             throws IllegalAlphabetException

Deprecated.

The naming of this method is confusing and inconsistent use either DNATools.toRNA(SymbolList list) or DNATools.transcribeToRNA(SymbolList list) depending on the desired behaivour.

Transcribe DNA into RNA.

Parameters:

list - the SymbolList to transcribe

Returns:

a SymbolList that is the transcribed view

Throws:

IllegalAlphabetException - if the list is not DNA

complementTable

public static ReversibleTranslationTable complementTable()

Get a translation table for complementing DNA symbols.

Since:

1.1

transcriptionTable

public static ReversibleTranslationTable transcriptionTable()

Get a translation table for converting DNA to RNA.

Since:

1.1

getGeneticCode

public static ManyToOneTranslationTable getGeneticCode(String name)

Retrieve a TranslationTable by name. The valid names are:

• "UNIVERSAL"
• "VERTEBRATE_MITOCHONDRIAL"
• "YEAST_MITOCHONDRIAL"
• "MOLD_MITOCHONDRIAL"
• "INVERTEBRATE_MITOCHONDRIAL"
• "CILIATE_NUCLEAR"
• "ECHINODERM_MITOCHONDRIAL"
• "EUPLOTID_NUCLEAR"
• "BACTERIAL"
• "ALTERNATIVE_YEAST_NUCLEAR"
• "ASCIDIAN_MITOCHONDRIAL"
• "FLATWORM_MITOCHONDRIAL"
• "BLEPHARISMA_MACRONUCLEAR"
• "CHLOROPHYCEAN_MITOCHONDRIAL"
• "TREMATODE_MITOCHONDRIAL"
• "SCENEDESMUS_MITOCHONDRIAL"

There are public static final fields in the TranslationTable interface which contain these values. One of these should be used as the argument for this method.

You can now get the reverse translation of the residue back to its (usually several) codons too.

Since:

1.1

getGeneticCode

public static ManyToOneTranslationTable getGeneticCode(int table_num)

Retrieve a TranslationTable by number. These numbers correspond to the transl_table qualifier in the DDBJ/EMBL/GenBank Feature Table (Version 6.5 Apr 2006): transl_table defines the genetic code table used if other than the universal genetic code table. Tables are described in appendix V, section 7.5.5:

• " 1 - UNIVERSAL"
• " 2 - VERTEBRATE_MITOCHONDRIAL"
• " 3 - YEAST_MITOCHONDRIAL"
• " 4 - MOLD_MITOCHONDRIAL"
• " 5 - INVERTEBRATE_MITOCHONDRIAL"
• " 6 - CILIATE_NUCLEAR"
• " 9 - ECHINODERM_MITOCHONDRIAL"
• "10 - EUPLOTID_NUCLEAR"
• "11 - BACTERIAL"
• "12 - ALTERNATIVE_YEAST_NUCLEAR"
• "13 - ASCIDIAN_MITOCHONDRIAL"
• "14 - FLATWORM_MITOCHONDRIAL"
• "15 - BLEPHARISMA_MACRONUCLEAR"
• "16 - 2CHLOROPHYCEAN_MITOCHONDRIAL"
• "21 - TREMATODE_MITOCHONDRIAL"
• "23 - SCENEDESMUS_MITOCHONDRIAL"

Throws:

IllegalArgumentException - if there is no table with that number.

Since:

1.5

getGeneticCodeNames

public static Set getGeneticCodeNames()

Retrieve a Set containing the name of each genetic code.

Since:

1.1

translate

public static SymbolList translate(SymbolList syms)
                            throws IllegalAlphabetException

Translate RNA into protein (with termination symbols). For compatibility with BioJava 1.1, this will also handle sequences which are already expressed in the (RNA x RNA x RNA) (codon) alphabet.

Throws:

IllegalAlphabetException

Since:

1.1