info.bioinfweb.commons.bio

Class SequenceUtils

java.lang.Object

info.bioinfweb.commons.bio.SequenceUtils

public class SequenceUtils
extends java.lang.Object

Useful tools to manipulate nucleotide and amino acid sequences stored as character sequences.

Author:

Ben Stöver

Field Summary

Fields

Modifier and Type	Field and Description
static java.lang.String	ALL_DNA_CHARS
static java.lang.String	ALL_RNA_CHARS
static java.lang.String	DNA_CHARS
static char	GAP_CHAR
static char	MATCH_CHAR
static char	MISSING_DATA_CHAR
static java.lang.String	RNA_CHARS
static char	STOP_CODON_CHAR

Constructor Summary

Constructors

Constructor and Description
SequenceUtils()

Method Summary

Modifier and Type	Method and Description
static char	aminoAcidConsensus(java.lang.String[] alignmentColumn)
static java.util.Map<java.lang.Character,java.lang.Double>	aminoAcidFrequencies(java.lang.String[] alignmentColumn)
static char	complement(char c) Returns the complement of the specified character.
static java.lang.String	complement(java.lang.CharSequence sequence) Returns the complementing sequence.
static java.lang.String	deleteAllGaps(java.lang.CharSequence seq) Returns the specified sequence without any gaps.
static java.lang.String	deleteFromLeft(java.lang.String seq, int count) Deletes count characters from the left side of the sequence which are not gaps ("-").
static java.lang.String	deleteFromRight(java.lang.String seq, int count) Deletes count characters from the left side of the sequence which are not gaps ("-").
static java.lang.String	deleteGapsFromLeft(java.lang.String seq, int count) Deletes the specified number of gaps from the sequence starting on the left side.
static java.lang.String	deleteGapsFromRight(java.lang.String seq, int count) Deletes the specified number of gaps from the sequence starting on the right side.
static java.lang.String	deleteLeadingGaps(java.lang.String seq) Deletes all leading gaps from a sequence.
static java.lang.String	deleteLeadingTrailingGaps(java.lang.String seq) Deletes all leading and trailing gaps of the specified sequence.
static java.lang.String	deleteTrailingGaps(java.lang.String seq) Deletes all trailing gaps from a sequence.
static java.lang.String	dnaToRNA(java.lang.String dna)
static java.util.Set<java.lang.Character>	getAminoAcidOneLetterCodes(boolean includeAmbiguity) Returns a set of all amino acid one letter codes in upper case.
static java.util.Set<java.lang.String>	getAminoAcidThreeLetterCodes(boolean includeAmbiguity) Returns a set of all amino acid three letter codes in upper case.
static java.util.Set<java.lang.Character>	getNucleotideCharacters() Returns a set of all nucleotide characters, including 'T' and 'U' as well as all IUPAC ambiguity codes in upper case.
static boolean	isAminoAcidAmbiguityCode(java.lang.String code) Determines whether the specified character is an amino acid ambiguity code.
static boolean	isDNAChar(char c)
static boolean	isInTokenSet(char c, java.lang.String tokens)
static boolean	isNonAmbiguityAminoAcid(java.lang.String code)
static boolean	isNonAmbiguityNucleotide(char c)
static boolean	isNucleotideAmbuguityCode(char nucleotide) Determines whether the specified character is an IUPAC ambiguity code.
static boolean	isRNAChar(char c)
static java.lang.String	leftSubsequence(java.lang.String seq, int count) Returns the left subsequence with the specified length (which does not include gaps).
static int	lengthWOGaps(java.lang.CharSequence sequence)
static char	nucleotideConsensus(char[] alignmentColumn) Returns the nucleotide that occurs most often in the specified alignment row.
static char[]	nucleotideConstituents(char nucleotide) If the specified nucleotide is an IUPAC ambiguity code this method returns an array containing all nucleotides that could be represented by the code.
static java.util.Map<java.lang.Character,java.lang.Double>	nucleotideFrequencies(char[] alignmentColumn) Counts the nucleotide frequencies in the specified alignment column.
static char	oneLetterAminoAcidByThreeLetter(java.lang.String threeLetterCode) Converts the specified three letter amino acid code into a one letter representation.
static char[]	oneLetterAminoAcidConstituents(java.lang.String code) Returns the one letter amino acid representations of all compounds that could be represented by the specified ambiguity code.
static java.lang.String	randSequence(boolean dna, int length, double rateCG) Returns a sequence of random DNA or RNA characters.
static java.lang.String	randSequence(boolean dna, int length, double rateC, double rateG, double rateA) Returns a sequence of random DNA or RNA characters.
static java.lang.String	reverse(java.lang.CharSequence sequence) Returns the reverse of the specified sequence.
static java.lang.String	reverseComplement(java.lang.CharSequence sequence) Returns the reverse complemented sequence.
static java.lang.String	rightSubsequence(java.lang.String seq, int count) Returns the right subsequence with the specified length (which does not include gaps).
static char[]	rnaConstituents(char nucleotide)
static java.lang.String	rnaToDNA(java.lang.String rna)
static java.lang.String	threeLetterAminoAcidByOneLetter(char oneLetterCode) Converts the specified one letter amino acid code into a three letter representation.
static java.lang.String[]	threeLetterAminoAcidConstituents(java.lang.String code) Returns the three letter amino acid representations of all compounds that could be represented by the specified ambiguity code.

Methods inherited from class java.lang.Object

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

Field Detail

GAP_CHAR

public static final char GAP_CHAR

See Also:

Constant Field Values

MISSING_DATA_CHAR

public static final char MISSING_DATA_CHAR

See Also:

Constant Field Values

MATCH_CHAR

public static final char MATCH_CHAR

See Also:

Constant Field Values

STOP_CODON_CHAR

public static final char STOP_CODON_CHAR

See Also:

Constant Field Values

DNA_CHARS

public static final java.lang.String DNA_CHARS

See Also:

Constant Field Values

ALL_DNA_CHARS

public static final java.lang.String ALL_DNA_CHARS

See Also:

Constant Field Values

RNA_CHARS

public static final java.lang.String RNA_CHARS

See Also:

Constant Field Values

ALL_RNA_CHARS

public static final java.lang.String ALL_RNA_CHARS

See Also:

Constant Field Values

Constructor Detail

SequenceUtils

public SequenceUtils()

Method Detail

getNucleotideCharacters

public static java.util.Set<java.lang.Character> getNucleotideCharacters()

Returns a set of all nucleotide characters, including 'T' and 'U' as well as all IUPAC ambiguity codes in upper case.

Returns:

a new set with all nucleotide tokens

nucleotideConstituents

public static char[] nucleotideConstituents(char nucleotide)

If the specified nucleotide is an IUPAC ambiguity code this method returns an array containing all nucleotides that could be represented by the code.

Constituents returned for ambiguity code are always DNA nucleotides (thymine is always used instead of uracil). (Anyway, if 'U' is specified for nucleotide the returned array will contain 'U' as the only element and not 'T').

If the specified character is not an ambiguity code character, an empty array is returned.

Parameters:

nucleotide - the character that may be an ambiguity code

Returns:

an array of the nucleotides as upper case letters

rnaConstituents

public static char[] rnaConstituents(char nucleotide)

isNonAmbiguityNucleotide

public static boolean isNonAmbiguityNucleotide(char c)

isNucleotideAmbuguityCode

public static boolean isNucleotideAmbuguityCode(char nucleotide)

Determines whether the specified character is an IUPAC ambiguity code.

Parameters:

nucleotide - the character that may be an ambiguity code

Returns:

true of the specified character is a valid ambiguity code, false otherwise.

getAminoAcidOneLetterCodes

public static java.util.Set<java.lang.Character> getAminoAcidOneLetterCodes(boolean includeAmbiguity)

Returns a set of all amino acid one letter codes in upper case.

Parameters:

includeAmbiguity - Specify true here if amino acid ambiguity codes shall also be contained in the returned set or false if only unambiguous characters shall be contained.

Returns:

a new set of amino acid codes

getAminoAcidThreeLetterCodes

public static java.util.Set<java.lang.String> getAminoAcidThreeLetterCodes(boolean includeAmbiguity)

Returns a set of all amino acid three letter codes in upper case.

Parameters:

includeAmbiguity - Specify true here if amino acid ambiguity codes shall also be contained in the returned set or false if only unambiguous characters shall be contained.

Returns:

a new set of amino acid codes

oneLetterAminoAcidByThreeLetter

public static char oneLetterAminoAcidByThreeLetter(java.lang.String threeLetterCode)

Converts the specified three letter amino acid code into a one letter representation. Besides the defined amino acid codes this method also accepts any string which consists of one character that is repeated three times. (E.g. "---" would be converted to '-').

Parameters:

threeLetterCode - the three letter code to be converted

Returns:

the according three letter code in upper case

Throws:

java.lang.IllegalArgumentException - if the specified code is not a valid one letter amino acid code or a three character long repetition of the same character

threeLetterAminoAcidByOneLetter

public static java.lang.String threeLetterAminoAcidByOneLetter(char oneLetterCode)

Converts the specified one letter amino acid code into a three letter representation.

Parameters:

oneLetterCode - the one letter code to be converted

Returns:

the according three letter code where the first letter is in upper case (e.g. "Pro") if oneLetterCode was a valid amino acid representation or a string consisting of three repetitions of the specified character otherwise (E.g. '-' would be converted to "---".)

oneLetterAminoAcidConstituents

public static char[] oneLetterAminoAcidConstituents(java.lang.String code)

Returns the one letter amino acid representations of all compounds that could be represented by the specified ambiguity code.

Parameters:

code - the ambiguity one or three letter ambiguity code to be converted

Returns:

an array with the one letter representations of the respective amino acids or an empty array if code was not a valid ambiguity code

threeLetterAminoAcidConstituents

public static java.lang.String[] threeLetterAminoAcidConstituents(java.lang.String code)

Returns the three letter amino acid representations of all compounds that could be represented by the specified ambiguity code.

Parameters:

code - the ambiguity one or three letter ambiguity code to be converted

Returns:

an array with the three letter representations of the according amino acids or an empty array if code was not a valid ambiguity code

isNonAmbiguityAminoAcid

public static boolean isNonAmbiguityAminoAcid(java.lang.String code)

isAminoAcidAmbiguityCode

public static boolean isAminoAcidAmbiguityCode(java.lang.String code)

Determines whether the specified character is an amino acid ambiguity code.

Parameters:

code - the string that may be an ambiguity code (one and three letter codes are supported)

Returns:

true of the specified character is a valid amino acid ambiguity code, false otherwise.

reverse

public static java.lang.String reverse(java.lang.CharSequence sequence)

Returns the reverse of the specified sequence.

Parameters:

sequence - the source sequence

Returns:

the inverse sequence

complement

public static char complement(char c)

Returns the complement of the specified character. (IUPAC ambiguity codes are also supported.) If an undefined character is specified (e.g. "-") it is returned unchanged.

Parameters:

c - the nucleotide to be complemented

Returns:

the complemented nucleotide character in upper or lower case depending on c

complement

public static java.lang.String complement(java.lang.CharSequence sequence)

Returns the complementing sequence. Ambiguity codes are supported. Upper case and lower case characters are replaced by their according complements.

Parameters:

sequence - the sequence to be complemented

Returns:

always a DNA sequence (no matter if the input was RNA or not)

reverseComplement

public static java.lang.String reverseComplement(java.lang.CharSequence sequence)

Returns the reverse complemented sequence. Ambiguity codes are supported. Upper case and lower case characters are replaced by their according complements.

Parameters:

sequence - the sequence to be reverse complemented

Returns:

always a DNA sequence (no matter if the input was RNA or not)

rnaToDNA

public static java.lang.String rnaToDNA(java.lang.String rna)

dnaToRNA

public static java.lang.String dnaToRNA(java.lang.String dna)

isDNAChar

public static boolean isDNAChar(char c)

isRNAChar

public static boolean isRNAChar(char c)

isInTokenSet

public static boolean isInTokenSet(char c,
                                   java.lang.String tokens)

lengthWOGaps

public static int lengthWOGaps(java.lang.CharSequence sequence)

leftSubsequence

public static java.lang.String leftSubsequence(java.lang.String seq,
                                               int count)

Returns the left subsequence with the specified length (which does not include gaps).

If there are less than count characters in seq the whole sequence is returned.

Example: leftSubsequence("AT-A-GCCTG-CTG", 5) would return AT-A-GC

Parameters:

seq - the source sequence

count - the number characters that shall be contained in the returned subsequence (not including gaps)

Returns:

the left subsequence containing the specified number of characters and possibly additional gaps

rightSubsequence

public static java.lang.String rightSubsequence(java.lang.String seq,
                                                int count)

Returns the right subsequence with the specified length (which does not include gaps).

If there are less than count characters in seq the whole sequence is returned.

Example: rightSubsequence("AT-A-GCCTG-CTG", 5) would return TG-CTG

Parameters:

seq - the source sequence

count - the number characters that shall be contained in the returned subsequence (not including gaps)

Returns:

the right subsequence containing the specified number of characters and possibly additional gaps

deleteFromLeft

public static java.lang.String deleteFromLeft(java.lang.String seq,
                                              int count)

Deletes count characters from the left side of the sequence which are not gaps ("-").

Parameters:

seq - the original sequence

count - the number of characters to be removed

Returns:

the sequence without the deleted characters and gaps

deleteFromRight

public static java.lang.String deleteFromRight(java.lang.String seq,
                                               int count)

Deletes count characters from the left side of the sequence which are not gaps ("-").

Parameters:

seq - the original sequence

count - the number of characters to be removed

Returns:

the sequence without the deleted characters and gaps

deleteLeadingGaps

public static java.lang.String deleteLeadingGaps(java.lang.String seq)

Deletes all leading gaps from a sequence.

Parameters:

seq -

Returns:

deleteTrailingGaps

public static java.lang.String deleteTrailingGaps(java.lang.String seq)

Deletes all trailing gaps from a sequence.

Parameters:

seq -

Returns:

deleteGapsFromLeft

public static java.lang.String deleteGapsFromLeft(java.lang.String seq,
                                                  int count)

Deletes the specified number of gaps from the sequence starting on the left side. If the sequence contains less than the specified number of gaps a sequence without gaps is returned.

Parameters:

seq - the sequence that contains the gaps

count - the number of gaps to be removed

Returns:

the sequence with less gaps

deleteGapsFromRight

public static java.lang.String deleteGapsFromRight(java.lang.String seq,
                                                   int count)

Deletes the specified number of gaps from the sequence starting on the right side. If the sequence contains less than the specified number of gaps a sequence without gaps is returned.

Parameters:

seq - the sequence that contains the gaps

count - the number of gaps to be removed

Returns:

the sequence with less gaps

deleteLeadingTrailingGaps

public static java.lang.String deleteLeadingTrailingGaps(java.lang.String seq)

Deletes all leading and trailing gaps of the specified sequence.

Parameters:

seq -

Returns:

deleteAllGaps

public static java.lang.String deleteAllGaps(java.lang.CharSequence seq)

Returns the specified sequence without any gaps.

Parameters:

seq -

Returns:

randSequence

public static java.lang.String randSequence(boolean dna,
                                            int length,
                                            double rateC,
                                            double rateG,
                                            double rateA)

Returns a sequence of random DNA or RNA characters. (The three rates together have to be lower than 1. The rate for thymidine or uracil is determined from the others.)

Parameters:

dna - determines whether a DNA sequence shall be returned (RNA id false)

length - the length of the sequence

rateC - the rate for cytosine

rateG - the rate for guanine

rateA - the rate for adenine

Returns:

the random sequence

randSequence

public static java.lang.String randSequence(boolean dna,
                                            int length,
                                            double rateCG)

Returns a sequence of random DNA or RNA characters.

Parameters:

dna - determines whether a DNA sequence shall be returned (RNA id false)

length - the length of the sequence

rateCG - the rate for cytosine and guanine (must lower than 1)

Returns:

the random sequence

nucleotideFrequencies

public static java.util.Map<java.lang.Character,java.lang.Double> nucleotideFrequencies(char[] alignmentColumn)

Counts the nucleotide frequencies in the specified alignment column.

IUPAC ambiguity codes are supported and counted accordingly for several nucleotides. (Examples: N would be counted as 0.25 for each nucleotide, R would be counted as 0.5 for C and 0.5 for T.)

Parameters:

alignmentColumn - the contents of the alignment column from which the consensus shall be calculated

Returns:

a map with the nucleotides as keys and their frequencies as values

nucleotideConsensus

public static char nucleotideConsensus(char[] alignmentColumn)

Returns the nucleotide that occurs most often in the specified alignment row. IUPAC ambiguity codes are recognized and counted accordingly for several nucleotides.

Parameters:

alignmentColumn - the contents of the alignment column from which the consensus shall be calculated

Returns:

the most frequent nucleotide (If several nucleotides occur equally often, one of them is chosen arbitrarily.)

aminoAcidFrequencies

public static java.util.Map<java.lang.Character,java.lang.Double> aminoAcidFrequencies(java.lang.String[] alignmentColumn)

aminoAcidConsensus

public static char aminoAcidConsensus(java.lang.String[] alignmentColumn)