Entry: AAstat
Aliases: AAstat
Keywords: utilities
Description: To Get Some Protein Statistics
URL: ../../../library/seqinr/html/AAstat.html

Entry: AnoukResult
Aliases: AnoukResult
Keywords: datasets
Description: Expected numeric results for Ka and Ks computation
URL: ../../../library/seqinr/html/AnoukResult.html

Entry: EXP
Aliases: EXP
Keywords: datasets
Description: Vectors of coefficients to compute linear forms.
URL: ../../../library/seqinr/html/EXP.html

Entry: G+C Content
Aliases: GC GC1 GC2 GC3
Keywords: manip
Description: Calculates the fractional G+C content of nucleic acid sequences
URL: ../../../library/seqinr/html/GC.html

Entry: SEQINR.UTIL
Aliases: SEQINR.UTIL
Keywords: datasets
Description: utility data for seqinr
URL: ../../../library/seqinr/html/SEQINR.UTIL.html

Entry: SeqAcnucWeb
Aliases: SeqAcnucWeb as.SeqAcnucWeb is.SeqAcnucWeb parser.socket
Keywords: utilities
Description: Sequence coming from an ACNUC data bases located on the web
URL: ../../../library/seqinr/html/SeqAcnucWeb.html

Entry: SeqFastaAA
Aliases: SeqFastaAA is.SeqFastaAA as.SeqFastaAA summary.SeqFastaAA
Keywords: utilities
Description: AA sequence in Fasta Format
URL: ../../../library/seqinr/html/SeqFastaAA.html

Entry: SeqFastadna
Aliases: SeqFastadna is.SeqFastadna as.SeqFastadna summary.SeqFastadna
Keywords: utilities
Description: Class for DNA sequence in Fasta Format
URL: ../../../library/seqinr/html/SeqFastadna.html

Entry: SeqFrag
Aliases: SeqFrag is.SeqFrag as.SeqFrag
Keywords: utilities
Description: Class for sub-sequences
URL: ../../../library/seqinr/html/SeqFrag.html

Entry: a
Aliases: a
Keywords: utilities
Description: Converts amino-acid three-letter code into the one-letter one
URL: ../../../library/seqinr/html/a.html

Entry: aaa
Aliases: aaa
Keywords: utilities
Description: Converts amino-acid one-letter code into the three-letter one
URL: ../../../library/seqinr/html/aaa.html

Entry: aacost
Aliases: aacost
Keywords: datasets
Description: Aerobic cost of amino-acids in Escherichia coli and G+C classes
URL: ../../../library/seqinr/html/aacost.html

Entry: c2s
Aliases: c2s
Keywords: utilities
Description: conversion of a vector of chars into a string
URL: ../../../library/seqinr/html/c2s.html

Entry: chargaff
Aliases: chargaff
Keywords: datasets
Description: Base composition in ssDNA for 7 bacterial DNA
URL: ../../../library/seqinr/html/chargaff.html

Entry: choosebank
Aliases: choosebank removeTrailingSpaces
Keywords: manip
Description: To select a database structured under ACNUC and located on the web
URL: ../../../library/seqinr/html/choosebank.html

Entry: closebank
Aliases: closebank
Keywords: manip
Description: To close a remote ACNUC database
URL: ../../../library/seqinr/html/closebank.html

Entry: comp
Aliases: comp
Keywords: manip
Description: complement a nucleic sequence
URL: ../../../library/seqinr/html/comp.html

Entry: computePI
Aliases: computePI
Keywords: manip
Description: To Compute the Theoretical Isoelectric Point
URL: ../../../library/seqinr/html/computePI.html

Entry: count
Aliases: count
Keywords: manip
Description: Composition of dimer/trimer/etc nucleotides
URL: ../../../library/seqinr/html/count.html

Entry: dia.bactgensize
Aliases: dia.bactgensize
Keywords: utilities
Description: Distribution of bacterial genome size from GOLD
URL: ../../../library/seqinr/html/dia.bactgensize.html

Entry: dinucl
Aliases: dinucl
Keywords: datasets
Description: Mean zscore on 242 complete bacterial chromosomes
URL: ../../../library/seqinr/html/dinucl.html

Entry: dist.alignment
Aliases: dist.alignment
Keywords: manip
Description: Pairwise Distances from Aligned Protein or DNA/RNA Sequences
URL: ../../../library/seqinr/html/dist.alignment.html

Entry: dotchart.uco
Aliases: dotchart.uco
Keywords: hplot
Description: Cleveland plot for codon usage tables
URL: ../../../library/seqinr/html/dotchart.uco.html

Entry: ec999
Aliases: ec999
Keywords: datasets
Description: 999 coding sequences from E. coli
URL: ../../../library/seqinr/html/ec999.html

Entry: gb2fasta
Aliases: gb2fasta
Keywords: utilities
Description: conversion of GenBank file into fasta file
URL: ../../../library/seqinr/html/gb2fasta.html

Entry: gbk2g2
Aliases: gbk2g2
Keywords: utilities
Description: Conversion of a GenBank format file into a glimmer-like one
URL: ../../../library/seqinr/html/gbk2g2.html

Entry: get.db.growth
Aliases: get.db.growth dia.db.growth
Keywords: utilities
Description: Get the exponential growth of nucleic acid database content
URL: ../../../library/seqinr/html/get.db.growth.html

Entry: get.ncbi
Aliases: get.ncbi ncbi.fna.url ncbi.ptt.url ncbi.stats ncbi.gbk.url
Keywords: utilities
Description: Bacterial complete genome data from ncbi ftp site
URL: ../../../library/seqinr/html/get.ncbi.html

Entry: getAnnot
Aliases: getAnnot getAnnot.SeqAcnucWeb getAnnot.SeqFastadna getAnnot.SeqFastaAA getAnnot.default readAnnots.socket getAnnots
Keywords: utilities
Description: Generic Function to obtain annotation for a sequence
URL: ../../../library/seqinr/html/getAnnot.html

Entry: getFrag
Aliases: getFrag getFrag.SeqAcnucWeb getFrag.SeqFastadna getFrag.SeqFastaAA getFrag.SeqFrag getFrag.default
Keywords: utilities
Description: Generic Function to obtain a fragment of a sequence
URL: ../../../library/seqinr/html/getFrag.html

Entry: getKeyword
Aliases: getKeyword getKeyword.SeqAcnucWeb getKeywordsocket getKeyword.default
Keywords: manip
Description: Generic Function to get keyword(s) associated to a sequence
URL: ../../../library/seqinr/html/getKeyword.html

Entry: getLength
Aliases: getLength getLength.SeqAcnucWeb getLength.SeqFastadna getLength.SeqFastaAA getLength.SeqFrag getLength.default getAttributsocket
Keywords: utilities
Description: Generic Function To obtain the length of a sequence
URL: ../../../library/seqinr/html/getLength.html

Entry: getLocation
Aliases: getLocation getLocation.SeqAcnucWeb getLocation.default getLocationSocket getExon
Keywords: utilities
Description: Generic Function To obtain the Position of a Sequence on the Parent Sequence
URL: ../../../library/seqinr/html/getLocation.html

Entry: getName
Aliases: getName getName.SeqAcnucWeb getName.SeqFastadna getName.SeqFastaAA getName.SeqFrag getName.default
Keywords: utilities
Description: Generic Function To obtain the name of a sequence
URL: ../../../library/seqinr/html/getName.html

Entry: getSequence
Aliases: getSequence getSequence.SeqAcnucWeb getSequence.SeqFastadna getSequence.SeqFastaAA getSequence.SeqFrag getSequence.default getNumber.socket getSequenceSocket
Keywords: utilities
Description: Generic Function To Get a sequence
URL: ../../../library/seqinr/html/getSequence.html

Entry: getTrans
Aliases: getTrans getTrans.SeqAcnucWeb getTrans.SeqFastadna getTrans.SeqFastaAA getTrans.SeqFrag getTrans.default
Keywords: utilities
Description: Generic Function to translate a sequence
URL: ../../../library/seqinr/html/getTrans.html

Entry: getType
Aliases: getType
Keywords: utilities
Description: To Get Sequence Type
URL: ../../../library/seqinr/html/getType.html

Entry: invers
Aliases: invers
Keywords: manip
Description: invers
URL: ../../../library/seqinr/html/invers.html

Entry: kaks
Aliases: kaks
Keywords: manip
Description: to Get an Estimation of Ka and Ks
URL: ../../../library/seqinr/html/kaks.html

Entry: lseqinr
Aliases: lseqinr
Keywords: utilities
Description: To see what's inside the package seqinr
URL: ../../../library/seqinr/html/lseqinr.html

Entry: n2s
Aliases: n2s
Keywords: utilities
Description: function to convert the numeric encoding of a DNA sequence into a vector of characters
URL: ../../../library/seqinr/html/n2s.html

Entry: oriloc
Aliases: oriloc
Keywords: utilities
Description: Prediction of origin and terminus of replication in bacteria
URL: ../../../library/seqinr/html/oriloc.html

Entry: permutation
Aliases: permutation
Keywords: utilities
Description: Sequence permutation according to several different models
URL: ../../../library/seqinr/html/permutation.html

Entry: plot.SeqAcnucWeb
Aliases: plot.SeqAcnucWeb
Keywords: hplot
Description: To Plot Subsequences on the Parent Sequence
URL: ../../../library/seqinr/html/plot.SeqAcnucWeb.html

Entry: prochlo
Aliases: prochlo
Keywords: datasets
Description: Zscore on three strains of Prochlorococcus marinus
URL: ../../../library/seqinr/html/prochlo.html

Entry: query
Aliases: query print.qaw simon
Keywords: utilities
Description: To get a list of sequence names from an ACNUC data base located on the web
URL: ../../../library/seqinr/html/query.html

Entry: read.alignment
Aliases: read.alignment
Keywords: manip
Description: Read aligned sequence files in mase, clustal, phylip, fasta or msf format
URL: ../../../library/seqinr/html/read.alignment.html

Entry: read.fasta
Aliases: read.fasta
Keywords: manip
Description: Read file in fasta format
URL: ../../../library/seqinr/html/read.fasta.html

Entry: s2c
Aliases: s2c
Keywords: utilities
Description: conversion of a string into a vector of chars
URL: ../../../library/seqinr/html/s2c.html

Entry: s2n
Aliases: s2n
Keywords: utilities
Description: simple numerical encoding of a DNA sequence.
URL: ../../../library/seqinr/html/s2n.html

Entry: splitseq
Aliases: splitseq
Keywords: manip
Description: split a sequence into sub-sequences
URL: ../../../library/seqinr/html/splitseq.html

Entry: syncodons
Aliases: syncodons
Keywords: utilities
Description: Synonymous codons
URL: ../../../library/seqinr/html/syncodons.html

Entry: synsequence
Aliases: synsequence
Keywords: utilities
Description: Random synonymous coding sequence generation
URL: ../../../library/seqinr/html/synsequence.html

Entry: tablecode
Aliases: tablecode
Keywords: utilities
Description: to plot genetic code as in textbooks
URL: ../../../library/seqinr/html/tablecode.html

Entry: toyaa
Aliases: toyaa
Keywords: datasets
Description: A toy example of amino-acid counts in three proteins
URL: ../../../library/seqinr/html/toyaa.html

Entry: toycodon
Aliases: toycodon
Keywords: datasets
Description: A toy example of codon counts in three coding sequences
URL: ../../../library/seqinr/html/toycodon.html

Entry: translate
Aliases: translate
Keywords: manip
Description: Translate nucleic acid sequences
URL: ../../../library/seqinr/html/translate.html

Entry: uco
Aliases: uco
Keywords: manip
Description: Codon usage indices
URL: ../../../library/seqinr/html/uco.html

Entry: ucoweight
Aliases: ucoweight
Keywords: utilities
Description: Weight of each synonymous codon
URL: ../../../library/seqinr/html/ucoweight.html

Entry: words
Aliases: words
Keywords: utilities
Description: To get all words from an alphabet.
URL: ../../../library/seqinr/html/words.html

Entry: words.pos
Aliases: words.pos
Keywords: utilities
Description: Positions of possibly degenerated motifs within sequences
URL: ../../../library/seqinr/html/words.pos.html

Entry: dinucleotides
Aliases: rho zscore
Keywords: utilities
Description: Statistical over- and under- representation of dinucleotides in a sequence
URL: ../../../library/seqinr/html/zscore.html
