String objects representing biological sequences, and matching algorithms


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Documentation for package `Biostrings' version 2.4.8

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

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

-- A --

AAString The AAString class
AAString-class The AAString class
AA_ALPHABET The AAString class
adjacentViews Constructor-like functions and generics for BStringViews objects
alignScore quadratic-space, simple gap implementation of Needleman-Wunsch global alignment algorithm
alphabet,AAString-method The AAString class
alphabet,BString-method The BString 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 --

blosum50 scoring matrix for codon substitution in protein alignments
BString The BString class
BString-class The BString class
BStringViews Constructor-like functions and generics for BStringViews objects
BStringViews,BString-method Constructor-like functions and generics for BStringViews objects
BStringViews,BStringViews-method Constructor-like functions and generics for BStringViews objects
BStringViews,file-method Constructor-like functions and generics for BStringViews objects
BStringViews-class The BStringViews class
BStringViews-constructors Constructor-like functions and generics for BStringViews objects

-- C --

class:AAString The AAString class
class:BString The BString 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
countPattern String searching functions
countPattern,ANY,BString-method String searching functions
countPattern,ANY,BStringViews-method String searching functions
countPattern,ANY,character-method String searching functions

-- D --

desc 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 --

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,BStringViews-method Constructor-like functions and generics for BStringViews objects
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
length,BString-method The BString class
length,BStringViews-method The BStringViews class
letter The BString class
letter,BString-method The BString class

-- 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
matchPattern String searching functions
matchPattern,ANY,BString-method String searching functions
matchPattern,ANY,BStringViews-method String searching functions
matchPattern,ANY,character-method String searching functions
matchProbePair Find "theoretical amplicons" mapped to a probe pair
matchProbePair,ANY,ANY,DNAString-method Find "theoretical amplicons" mapped to a probe pair
mismatch String searching functions
mismatch,ANY,BStringViews-method String searching functions

-- N --

nchar,BString-method The BString class
nchar,BStringViews-method The BStringViews class
needwunsQS 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 --

print.needwunsQS quadratic-space, simple gap implementation of Needleman-Wunsch global alignment algorithm

-- R --

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 --

show,BString-method The BString class
show,BStringViews-method The BStringViews class
start The BStringViews class
start,BStringViews-method The BStringViews class
subBString The BString class
subBString,BString-method The BString class
subject The BStringViews class
subject,BStringViews-method The BStringViews class
substr,BString-method The BString class
substring,BString-method The BString class

-- 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 Constructor-like functions and generics for BStringViews objects

-- W --

width The BStringViews class
width,BStringViews-method The BStringViews class
writeFASTA Functions to read/write FASTA formatted files
writeFASTA,BStringViews-method 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
[,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