String objects representing biological sequences, and matching algorithms


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Documentation for package ‘Biostrings’ version 2.6.6

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A B C D E F G I L M N P R S T V W Y misc

!=,BString,BString-method The BString class
!=,BString,BStringViews-method The BStringViews class
!=,BString,character-method The BString class
!=,BStringViews,BString-method The BStringViews class
!=,BStringViews,BStringViews-method The BStringViews class
!=,BStringViews,character-method The BStringViews class
!=,character,BString-method The BString class
!=,character,BStringViews-method The BStringViews class
==,BString,BString-method The BString class
==,BString,BStringViews-method The BStringViews class
==,BString,character-method The BString class
==,BStringViews,BString-method The BStringViews class
==,BStringViews,BStringViews-method The BStringViews class
==,BStringViews,character-method The BStringViews class
==,character,BString-method The BString class
==,character,BStringViews-method The BStringViews class

-- A --

AAString The AAString class
AAString-class The AAString class
AA_ALPHABET The AAString class
adjacentViews Basic functions for creating BStringViews objects
align1 The BStringAlign class
align1,BStringAlign-method The BStringAlign class
align2 The BStringAlign class
align2,BStringAlign-method The BStringAlign class
alignScore quadratic-space, simple gap implementation of Needleman-Wunsch global alignment algorithm
alphabet The BString class
alphabet,AAString-method The AAString class
alphabet,BString-method The BString class
alphabet,BStringAlign-method The BStringAlign class
alphabet,DNAString-method The DNAString class
alphabet,RNAString-method The RNAString class
alphabetFrequency Function to calculate the frequency of letters in a biological sequence
alphabetFrequency,BString-method Function to calculate the frequency of letters in a biological sequence
alphabetFrequency,BStringViews-method Function to calculate the frequency of letters in a biological sequence
alphabetFrequency,DNAString-method Function to calculate the frequency of letters in a biological sequence
alphabetFrequency,RNAString-method Function to calculate the frequency of letters in a biological sequence
AMINO_ACID_CODE The Single-Letter Amino Acid Code
as.character,BString-method The BString class
as.character,BStringViews-method The BStringViews class
as.complex,DNAString-method Converting a DNAString to a vector of complexes
as.list,BStringViews-method The BStringViews class
as.matrix,BStringViews-method The BStringViews class

-- B --

BLOSUM100 Scoring matrices
BLOSUM45 Scoring matrices
BLOSUM50 Scoring matrices
BLOSUM62 Scoring matrices
BLOSUM80 Scoring matrices
BString The BString class
BString-class The BString class
BStringAlign The BStringAlign class
BStringAlign-class The BStringAlign class
BStringPartialMatches-class The BStringPartialMatches class
BStringViews Basic functions for creating BStringViews objects
BStringViews,ANY-method Basic functions for creating BStringViews objects
BStringViews,BString-method Basic functions for creating BStringViews objects
BStringViews,BStringViews-method Basic functions for creating BStringViews objects
BStringViews,file-method Basic functions for creating BStringViews objects
BStringViews-class The BStringViews class
BStringViews-constructors Basic functions for creating BStringViews objects
BStringViewsToFASTArecords Input/output of BStringViews objects

-- C --

CharacterToFASTArecords Input/output of BStringViews objects
class:AAString The AAString class
class:BString The BString class
class:BStringAlign The BStringAlign class
class:BStringPartialMatches The BStringPartialMatches class
class:BStringViews The BStringViews class
class:DNAString The DNAString class
class:RNAString The RNAString class
complement Sequence reversing and complementing
complement,BStringViews-method Sequence reversing and complementing
complement,DNAString-method Sequence reversing and complementing
consmat Utility functions related to sequence alignment
consmat,BStringViews-method Utility functions related to sequence alignment
consmat,character-method Utility functions related to sequence alignment
consmat,list-method Utility functions related to sequence alignment
consmat,matrix-method Utility functions related to sequence alignment
countPattern String searching functions
countPattern,BString-method String searching functions
countPattern,BStringViews-method String searching functions
countPattern,character-method String searching functions

-- D --

desc The BStringViews class
desc,BStringViews-method The BStringViews class
desc<-,BStringViews-method The BStringViews class
DNAString The DNAString class
DNAString-class The DNAString class
DNA_ALPHABET The DNAString class

-- E --

end The BStringViews class
end,BStringViews-method The BStringViews class

-- F --

FASTArecordsToBStringViews Input/output of BStringViews objects
FASTArecordsToCharacter Input/output of BStringViews objects
findPalindromes Searching a sequence for palindromes
findPalindromes,BString-method Searching a sequence for palindromes
findPalindromes,BStringViews-method Searching a sequence for palindromes
first The BStringViews class
first,BStringViews-method The BStringViews class

-- G --

GENETIC_CODE The Standard Genetic Code
gregexpr2 A replacement for R standard gregexpr function

-- I --

initialize,AAString-method The AAString class
initialize,BString-method The BString class
initialize,BStringAlign-method The BStringAlign class
initialize,DNAString-method The DNAString class
initialize,RNAString-method The RNAString class
IUPAC_CODE_MAP The IUPAC Extended Genetic Alphabet

-- L --

last The BStringViews class
last,BStringViews-method The BStringViews class
lcprefix Longest Common Prefix/Suffix/Substring searching functions
lcprefix,BString,BString-method Longest Common Prefix/Suffix/Substring searching functions
lcprefix,BString,character-method Longest Common Prefix/Suffix/Substring searching functions
lcprefix,character,BString-method Longest Common Prefix/Suffix/Substring searching functions
lcprefix,character,character-method Longest Common Prefix/Suffix/Substring searching functions
lcsubstr Longest Common Prefix/Suffix/Substring searching functions
lcsubstr,BString,BString-method Longest Common Prefix/Suffix/Substring searching functions
lcsubstr,BString,character-method Longest Common Prefix/Suffix/Substring searching functions
lcsubstr,character,BString-method Longest Common Prefix/Suffix/Substring searching functions
lcsubstr,character,character-method Longest Common Prefix/Suffix/Substring searching functions
lcsuffix Longest Common Prefix/Suffix/Substring searching functions
lcsuffix,BString,BString-method Longest Common Prefix/Suffix/Substring searching functions
lcsuffix,BString,character-method Longest Common Prefix/Suffix/Substring searching functions
lcsuffix,character,BString-method Longest Common Prefix/Suffix/Substring searching functions
lcsuffix,character,character-method Longest Common Prefix/Suffix/Substring searching functions
length,BString-method The BString class
length,BStringAlign-method The BStringAlign class
length,BStringViews-method The BStringViews class
letter Subsetting a string
letter,BString-method Subsetting a string
letter,BStringViews-method Subsetting a string
letter,character-method Subsetting a string

-- M --

mask Masking portions of a sequence
mask,BString-method Masking portions of a sequence
mask,BStringViews-method Masking portions of a sequence
mask,character-method Masking portions of a sequence
matchDNAPattern String searching functions
matchLRPatterns Find patterns defined by a left and a right part in a sequence
matchLRPatterns,BString-method Find patterns defined by a left and a right part in a sequence
matchPattern String searching functions
matchPattern,BString-method String searching functions
matchPattern,BStringViews-method String searching functions
matchPattern,character-method String searching functions
matchProbePair Find "theoretical amplicons" mapped to a probe pair
matchProbePair,DNAString-method Find "theoretical amplicons" mapped to a probe pair
mismatch String searching functions
mismatch,BStringViews-method String searching functions

-- N --

nchar,BString-method The BString class
nchar,BStringAlign-method The BStringAlign class
nchar,BStringViews-method The BStringViews class
needwunsQS quadratic-space, simple gap implementation of Needleman-Wunsch global alignment algorithm
needwunsQS,BString,BString-method quadratic-space, simple gap implementation of Needleman-Wunsch global alignment algorithm
needwunsQS,BString,character-method quadratic-space, simple gap implementation of Needleman-Wunsch global alignment algorithm
needwunsQS,character,BString-method quadratic-space, simple gap implementation of Needleman-Wunsch global alignment algorithm
needwunsQS,character,character-method quadratic-space, simple gap implementation of Needleman-Wunsch global alignment algorithm

-- P --

palindromeArmLength Searching a sequence for palindromes
palindromeArmLength,BString-method Searching a sequence for palindromes
palindromeArmLength,BStringViews-method Searching a sequence for palindromes
palindromeLeftArm Searching a sequence for palindromes
palindromeLeftArm,BString-method Searching a sequence for palindromes
palindromeLeftArm,BStringViews-method Searching a sequence for palindromes
palindromeRightArm Searching a sequence for palindromes
palindromeRightArm,BString-method Searching a sequence for palindromes
palindromeRightArm,BStringViews-method Searching a sequence for palindromes
PAM120 Scoring matrices
PAM250 Scoring matrices
PAM30 Scoring matrices
PAM40 Scoring matrices
PAM70 Scoring matrices
pattern The BStringPartialMatches class
pattern,BStringPartialMatches-method The BStringPartialMatches class
pmatchPattern Longest Common Prefix/Suffix/Substring searching functions
pmatchPattern,BString-method Longest Common Prefix/Suffix/Substring searching functions
pmatchPattern,BStringViews-method Longest Common Prefix/Suffix/Substring searching functions
pmatchPattern,character-method Longest Common Prefix/Suffix/Substring searching functions
print.needwunsQS quadratic-space, simple gap implementation of Needleman-Wunsch global alignment algorithm

-- R --

read.BStringViews Input/output of BStringViews objects
readFASTA Functions to read/write FASTA formatted files
reverse Sequence reversing and complementing
reverse,BString-method Sequence reversing and complementing
reverse,BStringViews-method Sequence reversing and complementing
reverseComplement Sequence reversing and complementing
reverseComplement,BStringViews-method Sequence reversing and complementing
reverseComplement,DNAString-method Sequence reversing and complementing
RNAString The RNAString class
RNAString-class The RNAString class
RNA_ALPHABET The RNAString class

-- S --

score The BStringAlign class
score,BStringAlign-method The BStringAlign class
scoring.matrices Scoring matrices
show,BString-method The BString class
show,BStringAlign-method The BStringAlign class
show,BStringPartialMatches-method The BStringPartialMatches class
show,BStringViews-method The BStringViews class
start The BStringViews class
start,BStringViews-method The BStringViews class
subBString Fast substring extraction
subject The BStringViews class
subject,BStringViews-method The BStringViews class
subpatterns The BStringPartialMatches class
subpatterns,BStringPartialMatches-method The BStringPartialMatches class
substr Fast substring extraction
substr,BString-method Fast substring extraction
substr,BStringViews-method Fast substring extraction
substring Fast substring extraction
substring,BString-method Fast substring extraction
substring,BStringViews-method Fast substring extraction
subviews Fast substring extraction

-- T --

toComplex Converting a DNAString to a vector of complexes
toComplex,DNAString-method Converting a DNAString to a vector of complexes
toString,BString-method The BString class
toString,BStringViews-method The BStringViews class

-- V --

views Basic functions for creating BStringViews objects

-- W --

width The BStringViews class
width,BStringViews-method The BStringViews class
write.BStringViews Input/output of BStringViews objects
writeFASTA Functions to read/write FASTA formatted files

-- Y --

yeastSEQCHR1 An annotation data file for CHR1 in the yeastSEQ package

-- misc --

[,BString-method The BString class
[,BStringPartialMatches-method The BStringPartialMatches class
[,BStringViews-method The BStringViews class
[<-,BString-method The BString class
[<-,BStringViews-method The BStringViews class
[[,BStringViews-method The BStringViews class
[[<-,BStringViews-method The BStringViews class