R : Copyright 2005, The R Foundation for Statistical Computing
Version 2.1.1  (2005-06-20), ISBN 3-900051-07-0

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for a HTML browser interface to help.
Type 'q()' to quit R.

> ### * <HEADER>
> ###
> attach(NULL, name = "CheckExEnv")
> assign(".CheckExEnv", as.environment(2), pos = length(search())) # base
> ## add some hooks to label plot pages for base and grid graphics
> setHook("plot.new", ".newplot.hook")
> setHook("persp", ".newplot.hook")
> setHook("grid.newpage", ".gridplot.hook")
> 
> assign("cleanEx",
+        function(env = .GlobalEnv) {
+ 	   rm(list = ls(envir = env, all.names = TRUE), envir = env)
+            RNGkind("default", "default")
+ 	   set.seed(1)
+    	   options(warn = 1)
+ 	   delayedAssign("T", stop("T used instead of TRUE"),
+ 		  assign.env = .CheckExEnv)
+ 	   delayedAssign("F", stop("F used instead of FALSE"),
+ 		  assign.env = .CheckExEnv)
+ 	   sch <- search()
+ 	   newitems <- sch[! sch %in% .oldSearch]
+ 	   for(item in rev(newitems))
+                eval(substitute(detach(item), list(item=item)))
+ 	   missitems <- .oldSearch[! .oldSearch %in% sch]
+ 	   if(length(missitems))
+ 	       warning("items ", paste(missitems, collapse=", "),
+ 		       " have been removed from the search path")
+        },
+        env = .CheckExEnv)
> assign("..nameEx", "__{must remake R-ex/*.R}__", env = .CheckExEnv) # for now
> assign("ptime", proc.time(), env = .CheckExEnv)
> grDevices::postscript("seqinr-Examples.ps")
> assign("par.postscript", graphics::par(no.readonly = TRUE), env = .CheckExEnv)
> options(contrasts = c(unordered = "contr.treatment", ordered = "contr.poly"))
> options(warn = 1)    
> library('seqinr')
> 
> assign(".oldSearch", search(), env = .CheckExEnv)
> assign(".oldNS", loadedNamespaces(), env = .CheckExEnv)
> cleanEx(); ..nameEx <- "AAstat"
> 
> ### * AAstat
> 
> flush(stderr()); flush(stdout())
> 
> ### Name: AAstat
> ### Title: To Get Some Protein Statistics
> ### Aliases: AAstat
> ### Keywords: utilities
> 
> ### ** Examples
> 
>   ss = read.fasta(File=system.file("sequences/seqAA.fasta",package = "seqinr"),seqtype="AA")
>   AAstat(ss[[1]])
$Compo

 *  A  C  D  E  F  G  H  I  K  L  M  N  P  Q  R  S  T  V  W  Y 
 1  8  6  6 18  6  8  1  9 14 29  5  7 10  9 13 16  7  6  3  1 

$Prop
$Prop$Tiny
[1] 0.2459016

$Prop$Small
[1] 0.4043716

$Prop$Aliphatic
[1] 0.2404372

$Prop$Aromatic
[1] 0.06010929

$Prop$Non.polar
[1] 0.4972678

$Prop$Polar
[1] 0.4972678

$Prop$Charged
[1] 0.284153

$Prop$Basic
[1] 0.1530055

$Prop$Acidic
[1] 0.1311475


$Pi
[1] 8.534902

> 
> 
> 
> cleanEx(); ..nameEx <- "EXP"
> 
> ### * EXP
> 
> flush(stderr()); flush(stdout())
> 
> ### Name: EXP
> ### Title: Vectors of coefficients to compute linear forms.
> ### Aliases: EXP
> ### Keywords: datasets
> 
> ### ** Examples
> 
> data(EXP)
> 
> 
> 
> cleanEx(); ..nameEx <- "GC"
> 
> ### * GC
> 
> flush(stderr()); flush(stdout())
> 
> ### Name: GC
> ### Title: Calculates the fractional GC content of nucleic acid sequences
> ### Aliases: GC
> ### Keywords: manip
> 
> ### ** Examples
> 
>    s=s2c("agtctggggggccccttttaagtagatagatagctagtcgta")
>    GC(s)
[1] 0.4761905
> 
> 
> 
> cleanEx(); ..nameEx <- "GC2"
> 
> ### * GC2
> 
> flush(stderr()); flush(stdout())
> 
> ### Name: GC2
> ### Title: Calculates the fractional GC2 content of nucleic acid sequences
> ### Aliases: GC2
> ### Keywords: manip
> 
> ### ** Examples
> 
>    s=s2c("agtctggggggccccttttaagtagatagatagctagtcgta")
>    GC2(s)
[1] 0.357
> 
> 
> 
> cleanEx(); ..nameEx <- "GC3"
> 
> ### * GC3
> 
> flush(stderr()); flush(stdout())
> 
> ### Name: GC3
> ### Title: Calculates the fractional GC3 content of nucleic acid sequences
> ### Aliases: GC3
> ### Keywords: manip
> 
> ### ** Examples
> 
>    s=s2c("agtctggggggccccttttaagtagatagatagctagtcgta")
>    GC3(s)
[1] 0.4284
> 
> 
> 
> cleanEx(); ..nameEx <- "SEQINR.UTIL"
> 
> ### * SEQINR.UTIL
> 
> flush(stderr()); flush(stdout())
> 
> ### Name: SEQINR.UTIL
> ### Title: utility data for seqinr
> ### Aliases: SEQINR.UTIL
> ### Keywords: datasets
> 
> ### ** Examples
> 
> data(SEQINR.UTIL)
> 
> 
> 
> cleanEx(); ..nameEx <- "SeqAcnucWeb"
> 
> ### * SeqAcnucWeb
> 
> flush(stderr()); flush(stdout())
> 
> ### Name: SeqAcnucWeb
> ### Title: Sequence coming from an ACNUC data bases located on the web
> ### Aliases: SeqAcnucWeb as.SeqAcnucWeb is.SeqAcnucWeb parser.socket
> ### Keywords: utilities
> 
> ### ** Examples
> 
>   ## Not run: s = choosebank.socket("genbank")
>   ## Not run: query.socket(s$socket,"felis","sp=felis catus et t=cds et o=mitochondrion")
>   ## Not run: is.SeqAcnucWeb(felis$req[[1]])
> 
> 
> 
> cleanEx(); ..nameEx <- "SeqFastaAA"
> 
> ### * SeqFastaAA
> 
> flush(stderr()); flush(stdout())
> 
> ### Name: SeqFastaAA
> ### Title: AA sequence in Fasta Format
> ### Aliases: SeqFastaAA is.SeqFastaAA as.SeqFastaAA summary.SeqFastaAA
> ### Keywords: utilities
> 
> ### ** Examples
> 
>   s = read.fasta(File=system.file("sequences/seqAA.fasta",package="seqinr"),seqtype="AA")
>   is.SeqFastaAA(s[[1]])
[1] TRUE
>   summary(s[[1]])
$length
[1] 183

$composition

          *           A           C           D           E           F 
0.005464481 0.043715847 0.032786885 0.032786885 0.098360656 0.032786885 
          G           H           I           K           L           M 
0.043715847 0.005464481 0.049180328 0.076502732 0.158469945 0.027322404 
          N           P           Q           R           S           T 
0.038251366 0.054644809 0.049180328 0.071038251 0.087431694 0.038251366 
          V           W           Y 
0.032786885 0.016393443 0.005464481 

$AA.Property
$AA.Property$Tiny
[1] 0.2459016

$AA.Property$Small
[1] 0.4043716

$AA.Property$Aliphatic
[1] 0.2404372

$AA.Property$Aromatic
[1] 0.06010929

$AA.Property$Non.polar
[1] 0.4972678

$AA.Property$Polar
[1] 0.4972678

$AA.Property$Charged
[1] 0.284153

$AA.Property$Basic
[1] 0.1530055

$AA.Property$Acidic
[1] 0.1311475


>   myseq = s2c("MSPTAYRRGSPAFLV*")
>   as.SeqFastaAA(myseq, name = "myseq", Annot = "blablabla")
 [1] "M" "S" "P" "T" "A" "Y" "R" "R" "G" "S" "P" "A" "F" "L" "V" "*"
attr(,"name")
[1] "myseq"
attr(,"Annot")
[1] "blablabla"
attr(,"class")
[1] "SeqFastaAA"
>   myseq
 [1] "M" "S" "P" "T" "A" "Y" "R" "R" "G" "S" "P" "A" "F" "L" "V" "*"
> 
> 
> 
> cleanEx(); ..nameEx <- "SeqFastadna"
> 
> ### * SeqFastadna
> 
> flush(stderr()); flush(stdout())
> 
> ### Name: SeqFastadna
> ### Title: Class for DNA sequence in Fasta Format
> ### Aliases: SeqFastadna is.SeqFastadna as.SeqFastadna summary.SeqFastadna
> ### Keywords: utilities
> 
> ### ** Examples
> 
>  s = read.fasta(system.file("sequences/malM.fasta",package="seqinr"))
>  is.SeqFastadna(s[[1]])
[1] TRUE
>  summary(s[[1]])
$length
[1] 921

$composition

  a   c   g   t 
238 265 228 190 

$GC
[1] 0.5352877

>  myseq = s2c("acgttgatgctagctagcatcgat")
>  as.SeqFastadna(myseq, name = "myseq", Annot = "blablabla")
 [1] "a" "c" "g" "t" "t" "g" "a" "t" "g" "c" "t" "a" "g" "c" "t" "a" "g" "c" "a"
[20] "t" "c" "g" "a" "t"
attr(,"name")
[1] "myseq"
attr(,"Annot")
[1] "blablabla"
attr(,"class")
[1] "SeqFastadna"
>  myseq
 [1] "a" "c" "g" "t" "t" "g" "a" "t" "g" "c" "t" "a" "g" "c" "t" "a" "g" "c" "a"
[20] "t" "c" "g" "a" "t"
> 
> 
> 
> cleanEx(); ..nameEx <- "SeqFrag"
> 
> ### * SeqFrag
> 
> flush(stderr()); flush(stdout())
> 
> ### Name: SeqFrag
> ### Title: Class for sub-sequences
> ### Aliases: SeqFrag is.SeqFrag as.SeqFrag
> ### Keywords: utilities
> 
> ### ** Examples
> 
>  s = read.fasta(File=system.file("sequences/malM.fasta",package = "seqinr"))
>  getFrag(s[[1]],1,10)   
 [1] "a" "t" "g" "a" "a" "a" "a" "t" "g" "a"
attr(,"seqMother")
[1] "XYLEECOM.MALM"
attr(,"begin")
[1] 1
attr(,"end")
[1] 10
attr(,"class")
[1] "SeqFrag"
> 
> 
> 
> cleanEx(); ..nameEx <- "a"
> 
> ### * a
> 
> flush(stderr()); flush(stdout())
> 
> ### Name: a
> ### Title: Converts amino-acid three-letter code into the one-letter one
> ### Aliases: a
> ### Keywords: utilities
> 
> ### ** Examples
> 
>   # show all allowed values
>   allowed <- c("Stp", "Ala", "Cys", "Asp", "Glu", "Phe", "Gly", "His", "Ile",
+            "Lys", "Leu", "Met", "Asn", "Pro", "Gln", "Arg", "Ser", "Thr",
+            "Val", "Trp", "Tyr")
>   a(allowed)
 [1] "*" "A" "C" "D" "E" "F" "G" "H" "I" "K" "L" "M" "N" "P" "Q" "R" "S" "T" "V"
[20] "W" "Y"
>   # show what's happen with non-allowed values
>   a("SOS") # should be NA and a warning is generated
Warning in FUN(X[[1]], ...) : Unknown 3-letters code for aminoacid
[1] NA
> 
> 
> 
> cleanEx(); ..nameEx <- "aaa"
> 
> ### * aaa
> 
> flush(stderr()); flush(stdout())
> 
> ### Name: aaa
> ### Title: Converts amino-acid one-letter code into the three-letter one
> ### Aliases: aaa
> ### Keywords: utilities
> 
> ### ** Examples
> 
>   # show all allowed values
>   allowed <- s2c("*ACDEFGHIKLMNPQRSTVWY")
>   aaa(allowed)
 [1] "Stp" "Ala" "Cys" "Asp" "Glu" "Phe" "Gly" "His" "Ile" "Lys" "Leu" "Met"
[13] "Asn" "Pro" "Gln" "Arg" "Ser" "Thr" "Val" "Trp" "Tyr"
>   # show what's happen with non-allowed values
>   aaa("Z") # should be NA and a warning is generated
Warning in FUN(X[[1]], ...) : Unknown one letter code for aminoacid
[1] NA
> 
> 
> 
> cleanEx(); ..nameEx <- "c2s"
> 
> ### * c2s
> 
> flush(stderr()); flush(stdout())
> 
> ### Name: c2s
> ### Title: conversion of a vector of chars into a string
> ### Aliases: c2s
> ### Keywords: utilities
> 
> ### ** Examples
> 
> c2s( c("m","e","r","g","e","d") )
[1] "merged"
> 
> 
> 
> cleanEx(); ..nameEx <- "chargaff"
> 
> ### * chargaff
> 
> flush(stderr()); flush(stdout())
> 
> ### Name: chargaff
> ### Title: Base composition in ssDNA for 7 bacterial DNA
> ### Aliases: chargaff
> ### Keywords: datasets
> 
> ### ** Examples
> 
> data(chargaff)
> op <- par(no.readonly = TRUE)
> par(mfrow=c(4,4))
> xlim <- c(0,100)
> ylim <- xlim
> par(mai=rep(0,4))
> par(c(0.01, 0.99, 0.01, 0.99))
NULL
> par(xaxs="i")
> par(yaxs="i")
> 
> for( i in 1:4 )
+ {
+   for( j in 1:4 )
+   {
+     if( i == j )
+     {
+       plot(chargaff[,i], chargaff[,j],t="n", xlim=xlim, ylim=ylim,
+       xlab="", ylab="", xaxt="n", yaxt="n")
+       polygon(x=c(0,0,100,100),y=c(0,100,100,0), col="lightgrey")
+       for( k in seq(0,100,by=10) )
+       {
+         lseg <- 3
+         segments(k,0,k,lseg)
+         segments(k,100-lseg,k,100)
+         segments(0,k,lseg,k)
+         segments(100-lseg,k,100,k)
+       }
+       string <- paste(names(chargaff)[i],"\n\n",xlim[1],"% -",xlim[2],"%")
+       text(x=mean(xlim),y=mean(ylim), string, cex = 1.5)
+     }
+     else
+     {
+       plot(chargaff[,i], chargaff[,j], pch=20, xlim=xlim, ylim=ylim,
+       xlab="",ylab="", xaxt="n", yaxt="n")
+       iname <- names(chargaff)[i]
+       jname <- names(chargaff)[j]
+       direct <- function() segments(0,0,50,50, col="blue")
+       invers <- function() segments(0,50,50,0, col="blue")
+       PR2 <- function()
+       {
+         if( iname == "[A]" & jname == "[T]" ) { direct(); return() }
+         if( iname == "[T]" & jname == "[A]" ) { direct(); return() }
+         if( iname == "[C]" & jname == "[G]" ) { direct(); return() }
+         if( iname == "[G]" & jname == "[C]" ) { direct(); return() }
+         invers()
+       }
+       PR2()
+       polygon(x=c(0,100,100), y=c(100,100,0), col="lightpink")
+       polygon(x=c(0,0,100), y=c(0,100,0))
+     }
+   }
+ }
> # Clean up
> par(op)
> 
> 
> 
> graphics::par(get("par.postscript", env = .CheckExEnv))
> cleanEx(); ..nameEx <- "choosebank"
> 
> ### * choosebank
> 
> flush(stderr()); flush(stdout())
> 
> ### Name: choosebank
> ### Title: To select a database structured under ACNUC and located on the
> ###   web
> ### Aliases: choosebank
> ### Keywords: manip
> 
> ### ** Examples
> 
>   ## Not run:  mybank = choosebank() 
>   ## Not run:  choosebank(mybank[1]) 
> 
> 
> 
> cleanEx(); ..nameEx <- "comp"
> 
> ### * comp
> 
> flush(stderr()); flush(stdout())
> 
> ### Name: comp
> ### Title: complement a nucleic sequence
> ### Aliases: comp
> ### Keywords: manip
> 
> ### ** Examples
> 
>    a=s2c("acgtgctcgtatatatatgccc")
>    comp(a)              
 [1] "t" "g" "c" "a" "c" "g" "a" "g" "c" "a" "t" "a" "t" "a" "t" "a" "t" "a" "c"
[20] "g" "g" "g"
>    b=s2c("acgtXctcgtatatatatgccc")
>    comp(b)
 [1] "t" "g" "c" "a" NA  "g" "a" "g" "c" "a" "t" "a" "t" "a" "t" "a" "t" "a" "c"
[20] "g" "g" "g"
> 
> 
> 
> cleanEx(); ..nameEx <- "computePI"
> 
> ### * computePI
> 
> flush(stderr()); flush(stdout())
> 
> ### Name: computePI
> ### Title: To Compute the Theoretical Isoelectric Point
> ### Aliases: computePI
> ### Keywords: manip
> 
> ### ** Examples
> 
> ss = read.fasta(File=system.file("sequences/seqAA.fasta",package = "seqinr"),seqtype="AA")
> computePI(ss[[1]]) 
[1] 8.534902
> 
> 
> 
> cleanEx(); ..nameEx <- "count"
> 
> ### * count
> 
> flush(stderr()); flush(stdout())
> 
> ### Name: count
> ### Title: Composition of dimer/trimer/etc nucleotides
> ### Aliases: count
> ### Keywords: manip
> 
> ### ** Examples
> 
> a=s2c("acgggtacggtcccatcgaa")
> ##To count the occurences of dinucleotides of a:
> count(a,2)

aa ac ag at ca cc cg ct ga gc gg gt ta tc tg tt 
 1  2  0  1  1  2  3  0  1  0  3  2  1  2  0  0 
> ##To count the occurences of trinucleotides of a in frame 2:
> count(a,3,2)

aaa aac aag aat aca acc acg act aga agc agg agt ata atc atg att caa cac cag cat 
  0   0   0   0   0   0   1   0   0   0   0   0   0   1   0   0   0   0   0   1 
cca ccc ccg cct cga cgc cgg cgt cta ctc ctg ctt gaa gac gag gat gca gcc gcg gct 
  1   1   0   0   1   0   1   0   0   0   0   0   1   0   0   0   0   0   0   0 
gga ggc ggg ggt gta gtc gtg gtt taa tac tag tat tca tcc tcg tct tga tgc tgg tgt 
  0   0   1   2   1   1   0   0   0   1   0   0   0   1   1   0   0   0   0   0 
tta ttc ttg ttt 
  0   0   0   0 
> 
> 
> 
> cleanEx(); ..nameEx <- "dia.bactgensize"
> 
> ### * dia.bactgensize
> 
> flush(stderr()); flush(stdout())
> 
> ### Name: dia.bactgensize
> ### Title: Distribution of bacterial genome size from GOLD
> ### Aliases: dia.bactgensize
> ### Keywords: utilities
> 
> ### ** Examples
> 
>   ## Not run: dia.bactgensize()
> 
> 
> 
> cleanEx(); ..nameEx <- "dist.alignment"
> 
> ### * dist.alignment
> 
> flush(stderr()); flush(stdout())
> 
> ### Name: dist.alignment
> ### Title: Pairwise Distances from Aligned Protein or DNA/RNA Sequences
> ### Aliases: dist.alignment
> ### Keywords: manip
> 
> ### ** Examples
> 
>  s = read.alignment(File=system.file("sequences/test.mase", package = "seqinr"), format="mase")
>  dist.alignment( s, matrix = "identity" )
          Langur\r  Baboon\r   Human\r     Rat\r     Cow\r
Baboon\r 0.3307189                                        
Human\r  0.3750000 0.3307189                              
Rat\r    0.5448624 0.5077524 0.5376453                    
Cow\r    0.4921255 0.5448624 0.5590170 0.6495191          
Horse\r  0.7071068 0.7071068 0.7015608 0.7015608 0.7342088
> 
> 
> 
> cleanEx(); ..nameEx <- "dotchart.uco"
> 
> ### * dotchart.uco
> 
> flush(stderr()); flush(stdout())
> 
> ### Name: dotchart.uco
> ### Title: Cleveland plot for codon usage tables
> ### Aliases: dotchart.uco
> ### Keywords: hplot
> 
> ### ** Examples
> 
> # Load dataset:
> data(ec999)
> # Compute codon usage for all coding sequences:
> ec999.uco <- lapply(ec999, uco, index="eff") 
> # Put it in a dataframe:
> df <- as.data.frame(lapply(ec999.uco, as.vector)) 
> # Add codon names:
> row.names(df) <- names(ec999.uco[[1]])
> # Compute global codon usage:
> global <- rowSums(df)
> # Choose a title for the graph:
> title <- "Codon usage in 999 E. coli coding sequences"
> # Plot data:
> dotchart.uco(global, main = title) 
> 
> 
> 
> cleanEx(); ..nameEx <- "ec999"
> 
> ### * ec999
> 
> flush(stderr()); flush(stdout())
> 
> ### Name: ec999
> ### Title: 999 coding sequences from E. coli
> ### Aliases: ec999
> ### Keywords: datasets
> 
> ### ** Examples
> 
> data(ec999)
> 
> 
> 
> cleanEx(); ..nameEx <- "gb2fasta"
> 
> ### * gb2fasta
> 
> flush(stderr()); flush(stdout())
> 
> ### Name: gb2fasta
> ### Title: conversion of GenBank file into fasta file
> ### Aliases: gb2fasta
> ### Keywords: utilities
> 
> ### ** Examples
> 
> ## Not run: gb2fasta()
> 
> 
> 
> cleanEx(); ..nameEx <- "gbk2g2"
> 
> ### * gbk2g2
> 
> flush(stderr()); flush(stdout())
> 
> ### Name: gbk2g2
> ### Title: Conversion of a GenBank format file into a glimmer-like one
> ### Aliases: gbk2g2
> ### Keywords: utilities
> 
> ### ** Examples
> 
>  ## Not run:  gbk2g2() 
> 
> 
> 
> cleanEx(); ..nameEx <- "get.db.growth"
> 
> ### * get.db.growth
> 
> flush(stderr()); flush(stdout())
> 
> ### Name: get.db.growth
> ### Title: Get the exponential growth of nucleic acid database content
> ### Aliases: get.db.growth dia.db.growth
> ### Keywords: utilities
> 
> ### ** Examples
> 
> ## Not run: data <- get.db.growth()
> ## Not run: dia.db.growth(data)
> 
> 
> 
> cleanEx(); ..nameEx <- "get.ncbi"
> 
> ### * get.ncbi
> 
> flush(stderr()); flush(stdout())
> 
> ### Name: get.ncbi
> ### Title: Bacterial complete genome data from ncbi ftp site
> ### Aliases: get.ncbi ncbi.fna.url ncbi.ptt.url ncbi.stats ncbi.gbk.url
> ### Keywords: utilities
> 
> ### ** Examples
> 
> ## Not run: bacteria <- get.ncbi()
> ## Not run: summary(bacteria)
> 
> 
> 
> cleanEx(); ..nameEx <- "getAnnot"
> 
> ### * getAnnot
> 
> flush(stderr()); flush(stdout())
> 
> ### Name: getAnnot
> ### Title: Generic Function to obtain annotation for a sequence
> ### Aliases: getAnnot getAnnot.SeqAcnucWeb getAnnot.SeqFastadna
> ###   getAnnot.SeqFastaAA getAnnot.default readAnnots.socket getAnnots
> ### Keywords: utilities
> 
> ### ** Examples
> 
>   methods(getAnnot)
[1] getAnnot.SeqAcnucWeb getAnnot.SeqFastaAA  getAnnot.SeqFastadna
[4] getAnnot.default    
> 
> 
> 
> cleanEx(); ..nameEx <- "getFrag"
> 
> ### * getFrag
> 
> flush(stderr()); flush(stdout())
> 
> ### Name: getFrag
> ### Title: Generic Function to obtain a fragment of a sequence
> ### Aliases: getFrag getFrag.SeqAcnucWeb getFrag.SeqFastadna
> ###   getFrag.SeqFastaAA getFrag.SeqFrag getFrag.default
> ### Keywords: utilities
> 
> ### ** Examples
> 
>   methods(getFrag)
[1] getFrag.SeqAcnucWeb getFrag.SeqFastaAA  getFrag.SeqFastadna
[4] getFrag.SeqFrag     getFrag.default    
> 
> 
> 
> cleanEx(); ..nameEx <- "getKeyword"
> 
> ### * getKeyword
> 
> flush(stderr()); flush(stdout())
> 
> ### Name: getKeyword
> ### Title: Generic Function to get keyword(s) associated to a sequence
> ### Aliases: getKeyword getKeyword.SeqAcnucWeb getKeywordsocket
> ###   getKeyword.default
> ### Keywords: manip
> 
> ### ** Examples
> 
>  ## Not run: s=choosebank.socket("embl")
>  ## Not run: query.socket(s$socket,"fc","sp=felis catus et t=cds")
>  ## Not run: getKeyword(fc$req[[7]])
> 
> 
> 
> cleanEx(); ..nameEx <- "getLength"
> 
> ### * getLength
> 
> flush(stderr()); flush(stdout())
> 
> ### Name: getLength
> ### Title: Generic Function To obtain the length of a sequence
> ### Aliases: getLength getLength.SeqAcnucWeb getLength.SeqFastadna
> ###   getLength.SeqFastaAA getLength.SeqFrag getLength.default
> ###   getAttributsocket
> ### Keywords: utilities
> 
> ### ** Examples
> 
>  methods(getLength)
[1] getLength.SeqAcnucWeb getLength.SeqFastaAA  getLength.SeqFastadna
[4] getLength.SeqFrag     getLength.default    
> 
> 
> 
> cleanEx(); ..nameEx <- "getLocation"
> 
> ### * getLocation
> 
> flush(stderr()); flush(stdout())
> 
> ### Name: getLocation
> ### Title: Generic Function To obtain the Position of a Sequence on the
> ###   Parent Sequence
> ### Aliases: getLocation getLocation.SeqAcnucWeb getLocation.default
> ###   getLocationSocket getExon
> ### Keywords: utilities
> 
> ### ** Examples
> 
>   methods(getLocation)
[1] getLocation.SeqAcnucWeb getLocation.default    
> 
> 
> 
> cleanEx(); ..nameEx <- "getName"
> 
> ### * getName
> 
> flush(stderr()); flush(stdout())
> 
> ### Name: getName
> ### Title: Generic Function To obtain the name of a sequence
> ### Aliases: getName getName.SeqAcnucWeb getName.SeqFastadna
> ###   getName.SeqFastaAA getName.SeqFrag getName.default
> ### Keywords: utilities
> 
> ### ** Examples
> 
>   methods(getName)
[1] getName.SeqAcnucWeb getName.SeqFastaAA  getName.SeqFastadna
[4] getName.SeqFrag     getName.default    
> 
> 
> 
> cleanEx(); ..nameEx <- "getSequence"
> 
> ### * getSequence
> 
> flush(stderr()); flush(stdout())
> 
> ### Name: getSequence
> ### Title: Generic Function To Get a sequence
> ### Aliases: getSequence getSequence.SeqAcnucWeb getSequence.SeqFastadna
> ###   getSequence.SeqFastaAA getSequence.SeqFrag getSequence.default
> ###   getNumber.socket getSequenceSocket
> ### Keywords: utilities
> 
> ### ** Examples
> 
>  methods(getSequence)
[1] getSequence.SeqAcnucWeb getSequence.SeqFastaAA  getSequence.SeqFastadna
[4] getSequence.SeqFrag     getSequence.default    
> 
> 
> 
> cleanEx(); ..nameEx <- "getTrans"
> 
> ### * getTrans
> 
> flush(stderr()); flush(stdout())
> 
> ### Name: getTrans
> ### Title: Generic Function to translate a sequence
> ### Aliases: getTrans getTrans.SeqAcnucWeb getTrans.SeqFastadna
> ###   getTrans.SeqFastaAA getTrans.SeqFrag getTrans.default
> ### Keywords: utilities
> 
> ### ** Examples
> 
>  methods(getTrans)
[1] getTrans.SeqAcnucWeb getTrans.SeqFastadna getTrans.SeqFrag    
[4] getTrans.default    
> 
> 
> 
> cleanEx(); ..nameEx <- "getType"
> 
> ### * getType
> 
> flush(stderr()); flush(stdout())
> 
> ### Name: getType
> ### Title: To Get Sequence Type
> ### Aliases: getType
> ### Keywords: utilities
> 
> ### ** Examples
> 
> ## Not run: s = choosebank("genbank")
> ## Not run: geType(s$socket) 
> 
> 
> 
> cleanEx(); ..nameEx <- "invers"
> 
> ### * invers
> 
> flush(stderr()); flush(stdout())
> 
> ### Name: invers
> ### Title: invers
> ### Aliases: invers
> ### Keywords: manip
> 
> ### ** Examples
> 
> s=s2c("acgtgctcgtataatatgccc")
> invers(s)
 [1] "c" "c" "c" "g" "t" "a" "t" "a" "a" "t" "a" "t" "g" "c" "t" "c" "g" "t" "g"
[20] "c" "a"
> 
> 
> 
> cleanEx(); ..nameEx <- "kaks"
> 
> ### * kaks
> 
> flush(stderr()); flush(stdout())
> 
> ### Name: kaks
> ### Title: to Get an Estimation of Ka and Ks
> ### Aliases: kaks
> ### Keywords: manip
> 
> ### ** Examples
> 
> 
>  s = read.alignment(File=system.file("sequences/test.phylip", package = "seqinr"),format="phylip")
>  kaks(s)        
$ka
           Turkey     Salmo gair H. Sapiens Chimp     
Salmo gair   0.337238                                 
H. Sapiens   0.608861   0.510865                      
Chimp        0.914317   0.436320   9.999999           
Gorilla      0.886503   0.680707   0.570281   0.327377

$ks
           Turkey     Salmo gair H. Sapiens Chimp     
Salmo gair   0.332534                                 
H. Sapiens   0.692599   0.445049                      
Chimp        9.999999   9.999999   9.999999           
Gorilla      9.999999   9.999999   9.999999   0.137854

$vka
           Turkey     Salmo gair H. Sapiens Chimp     
Salmo gair   0.037473                                 
H. Sapiens   0.108237   0.120487                      
Chimp        0.184921   0.081530   9.999999           
Gorilla      0.529882   0.371615   0.353365   0.030199

$vks
           Turkey     Salmo gair H. Sapiens Chimp     
Salmo gair   0.185249                                 
H. Sapiens   0.645266   0.259180                      
Chimp        9.999999   9.999999   9.999999           
Gorilla      9.999999   9.999999   9.999999   0.058225

> 
> 
> 
> cleanEx(); ..nameEx <- "lseqinr"
> 
> ### * lseqinr
> 
> flush(stderr()); flush(stdout())
> 
> ### Name: lseqinr
> ### Title: To see what's inside the package seqinr
> ### Aliases: lseqinr
> ### Keywords: utilities
> 
> ### ** Examples
> 
> lseqinr()
  [1] "AAstat"                  "EXP"                    
  [3] "GC"                      "GC2"                    
  [5] "GC3"                     "SEQINR.UTIL"            
  [7] "a"                       "aaa"                    
  [9] "as.SeqAcnucWeb"          "as.SeqFastaAA"          
 [11] "as.SeqFastadna"          "as.SeqFrag"             
 [13] "c2s"                     "choosebank"             
 [15] "comp"                    "computePI"              
 [17] "count"                   "dia.bactgensize"        
 [19] "dia.db.growth"           "dist.alignment"         
 [21] "dotchart.uco"            "gb2fasta"               
 [23] "gbk2g2"                  "get.db.growth"          
 [25] "get.ncbi"                "getAnnot"               
 [27] "getAnnot.SeqAcnucWeb"    "getAnnot.SeqFastaAA"    
 [29] "getAnnot.SeqFastadna"    "getAnnot.default"       
 [31] "getAttributsocket"       "getFrag"                
 [33] "getFrag.SeqAcnucWeb"     "getFrag.SeqFastaAA"     
 [35] "getFrag.SeqFastadna"     "getFrag.SeqFrag"        
 [37] "getFrag.default"         "getKeyword"             
 [39] "getKeyword.SeqAcnucWeb"  "getKeyword.default"     
 [41] "getKeywordsocket"        "getLength"              
 [43] "getLength.SeqAcnucWeb"   "getLength.SeqFastaAA"   
 [45] "getLength.SeqFastadna"   "getLength.SeqFrag"      
 [47] "getLength.default"       "getLocation"            
 [49] "getLocation.SeqAcnucWeb" "getLocation.default"    
 [51] "getLocationSocket"       "getName"                
 [53] "getName.SeqAcnucWeb"     "getName.SeqFastaAA"     
 [55] "getName.SeqFastadna"     "getName.SeqFrag"        
 [57] "getName.default"         "getNumber.socket"       
 [59] "getSequence"             "getSequence.SeqAcnucWeb"
 [61] "getSequence.SeqFastaAA"  "getSequence.SeqFastadna"
 [63] "getSequence.SeqFrag"     "getSequence.default"    
 [65] "getSequenceSocket"       "getTrans"               
 [67] "getTrans.SeqAcnucWeb"    "getTrans.SeqFastadna"   
 [69] "getTrans.SeqFrag"        "getTrans.default"       
 [71] "getType"                 "invers"                 
 [73] "is.SeqAcnucWeb"          "is.SeqFastaAA"          
 [75] "is.SeqFastadna"          "is.SeqFrag"             
 [77] "kaks"                    "lseqinr"                
 [79] "n2s"                     "ncbi.fna.url"           
 [81] "ncbi.gbk.url"            "ncbi.ptt.url"           
 [83] "ncbi.stats"              "oriloc"                 
 [85] "parser.socket"           "plot.SeqAcnucWeb"       
 [87] "print.qaw"               "query"                  
 [89] "read.alignment"          "read.fasta"             
 [91] "readAnnots.socket"       "s2c"                    
 [93] "s2n"                     "splitseq"               
 [95] "summary.SeqFastaAA"      "summary.SeqFastadna"    
 [97] "tablecode"               "translate"              
 [99] "uco"                     "words"                  
[101] "words.pos"              
> 
> 
> 
> cleanEx(); ..nameEx <- "n2s"
> 
> ### * n2s
> 
> flush(stderr()); flush(stdout())
> 
> ### Name: n2s
> ### Title: function to convert the numeric encoding of a DNA sequence into
> ###   a vector of characters
> ### Aliases: n2s
> ### Keywords: utilities
> 
> ### ** Examples
> 
> ##example of the default behaviour:
> nseq <- sample(x = 0:3, size = 100, replace = TRUE)
> n2s(nseq) 
  [1] "c" "c" "g" "t" "a" "t" "t" "g" "g" "a" "a" "a" "g" "c" "t" "c" "g" "t"
 [19] "c" "t" "t" "a" "g" "a" "c" "c" "a" "c" "t" "c" "c" "g" "c" "a" "t" "g"
 [37] "t" "a" "g" "c" "t" "g" "t" "g" "g" "t" "a" "c" "g" "g" "c" "t" "c" "a"
 [55] "a" "a" "c" "g" "g" "c" "t" "c" "c" "c" "g" "c" "c" "t" "a" "t" "c" "t"
 [73] "c" "c" "c" "t" "t" "c" "t" "t" "c" "g" "c" "c" "t" "a" "g" "a" "a" "a"
 [91] "a" "a" "g" "t" "t" "t" "c" "c" "t" "g"
> # Show what's happen with out-of-range and NA values:
> nseq[1] <- NA
> nseq[2] <- 777
> n2s(nseq)[1:10]
 [1] NA  NA  "g" "t" "a" "t" "t" "g" "g" "a"
> # How to get an RNA instead:
> n2s(nseq, levels = c("a", "c", "g", "u"))
  [1] NA  NA  "g" "u" "a" "u" "u" "g" "g" "a" "a" "a" "g" "c" "u" "c" "g" "u"
 [19] "c" "u" "u" "a" "g" "a" "c" "c" "a" "c" "u" "c" "c" "g" "c" "a" "u" "g"
 [37] "u" "a" "g" "c" "u" "g" "u" "g" "g" "u" "a" "c" "g" "g" "c" "u" "c" "a"
 [55] "a" "a" "c" "g" "g" "c" "u" "c" "c" "c" "g" "c" "c" "u" "a" "u" "c" "u"
 [73] "c" "c" "c" "u" "u" "c" "u" "u" "c" "g" "c" "c" "u" "a" "g" "a" "a" "a"
 [91] "a" "a" "g" "u" "u" "u" "c" "c" "u" "g"
> 
> 
> 
> cleanEx(); ..nameEx <- "oriloc"
> 
> ### * oriloc
> 
> flush(stderr()); flush(stdout())
> 
> ### Name: oriloc
> ### Title: Prediction of origin and terminus of replication in bacteria
> ### Aliases: oriloc
> ### Keywords: utilities
> 
> ### ** Examples
> 
>   ## Not run:   out <- oriloc() 
>   ## Not run: 
> ##D   plot(out$st, out$sk, type="l", xlab="Map position in Kb",
> ##D     ylab = "Cumulated composite skew", 
> ##D     main=expression(italic(Chlamydia~~trachomatis)~~complete~~genome))
> ## End(Not run)
> 
> 
> 
> cleanEx(); ..nameEx <- "plot.SeqAcnucWeb"
> 
> ### * plot.SeqAcnucWeb
> 
> flush(stderr()); flush(stdout())
> 
> ### Name: plot.SeqAcnucWeb
> ### Title: To Plot Subsequences on the Parent Sequence
> ### Aliases: plot.SeqAcnucWeb
> ### Keywords: hplot
> 
> ### ** Examples
> 
> ## Not run:  s=choosebank("hovernucl")
> ## Not run:  query(s$socket,"list","sp=homo sapiens et k=globin@")        
> ## Not run:  plot.SeqAcnucWeb(list$req[[22]]) 
> ## Not run:  plot.SeqAcnucWeb(list$req[[22]],type=c("CDS","5'NCR")) 
> 
> 
> 
> cleanEx(); ..nameEx <- "query"
> 
> ### * query
> 
> flush(stderr()); flush(stdout())
> 
> ### Name: query
> ### Title: To get a list of sequence names from an ACNUC data base located
> ###   on the web
> ### Aliases: query print.qaw
> ### Keywords: utilities
> 
> ### ** Examples
> 
>  ## Not run: s = choosebank("genbank")
>  ## Not run: query(s$socket,"ecoli","sp=escherichia coli@")
>  ## Not run: ecoli
>  # To have the 4 first names of the sequence
>  ## Not run: ecoli$req[1:4]
>  ## Not run: ecoli$req[[5]]
>  ## Not run: ecoli$call
> 
> 
> 
> cleanEx(); ..nameEx <- "read.alignment"
> 
> ### * read.alignment
> 
> flush(stderr()); flush(stdout())
> 
> ### Name: read.alignment
> ### Title: Read file in mase, clustal, phylip, fasta or msf format
> ### Aliases: read.alignment
> ### Keywords: manip
> 
> ### ** Examples
> 
>         mase = read.alignment(File=system.file("sequences/test.mase",package = "seqinr"), format="mase")
>         phylip = read.alignment(File=system.file("sequences/test.phylip",package = "seqinr"), format="phylip")
>         msf = read.alignment(File=system.file("sequences/test.msf",package = "seqinr"), format="msf")
> 
> 
> 
> cleanEx(); ..nameEx <- "read.fasta"
> 
> ### * read.fasta
> 
> flush(stderr()); flush(stdout())
> 
> ### Name: read.fasta
> ### Title: Read file in fasta format
> ### Aliases: read.fasta
> ### Keywords: manip
> 
> ### ** Examples
> 
> s = read.fasta(File=system.file("sequences/malM.fasta",package = "seqinr"))
> ss = read.fasta(File=system.file("sequences/seqAA.fasta",package = "seqinr"),seqtype="AA")
> 
> 
> 
> cleanEx(); ..nameEx <- "s2c"
> 
> ### * s2c
> 
> flush(stderr()); flush(stdout())
> 
> ### Name: s2c
> ### Title: conversion of a string into a vector of chars
> ### Aliases: s2c
> ### Keywords: utilities
> 
> ### ** Examples
> 
> s2c( "BigBang" )
[1] "B" "i" "g" "B" "a" "n" "g"
> 
> 
> 
> cleanEx(); ..nameEx <- "s2n"
> 
> ### * s2n
> 
> flush(stderr()); flush(stdout())
> 
> ### Name: s2n
> ### Title: simple numerical encoding of a DNA sequence.
> ### Aliases: s2n
> ### Keywords: utilities
> 
> ### ** Examples
> 
> #example of default behaviour
> urndna <- c("a","c","g","t")
> seq <- sample( urndna, 100, replace = TRUE ) ; seq
  [1] "c" "c" "g" "t" "a" "t" "t" "g" "g" "a" "a" "a" "g" "c" "t" "c" "g" "t"
 [19] "c" "t" "t" "a" "g" "a" "c" "c" "a" "c" "t" "c" "c" "g" "c" "a" "t" "g"
 [37] "t" "a" "g" "c" "t" "g" "t" "g" "g" "t" "a" "c" "g" "g" "c" "t" "c" "a"
 [55] "a" "a" "c" "g" "g" "c" "t" "c" "c" "c" "g" "c" "c" "t" "a" "t" "c" "t"
 [73] "c" "c" "c" "t" "t" "c" "t" "t" "c" "g" "c" "c" "t" "a" "g" "a" "a" "a"
 [91] "a" "a" "g" "t" "t" "t" "c" "c" "t" "g"
> s2n(seq)
  [1] 1 1 2 3 0 3 3 2 2 0 0 0 2 1 3 1 2 3 1 3 3 0 2 0 1 1 0 1 3 1 1 2 1 0 3 2 3
 [38] 0 2 1 3 2 3 2 2 3 0 1 2 2 1 3 1 0 0 0 1 2 2 1 3 1 1 1 2 1 1 3 0 3 1 3 1 1
 [75] 1 3 3 1 3 3 1 2 1 1 3 0 2 0 0 0 0 0 2 3 3 3 1 1 3 2
attr(,"levels")
[1] "a" "c" "g" "t"
> #How to deal with RNA
> urnrna <- c("a","c","g","t")
> seq <- sample( urnrna, 100, replace = TRUE ) ; seq
  [1] "g" "c" "c" "t" "g" "a" "a" "c" "t" "g" "t" "g" "c" "c" "a" "a" "g" "a"
 [19] "c" "g" "t" "c" "c" "a" "t" "c" "g" "a" "a" "g" "g" "a" "a" "g" "t" "g"
 [37] "g" "g" "t" "g" "g" "g" "a" "c" "g" "c" "a" "g" "a" "t" "g" "g" "c" "c"
 [55] "g" "a" "g" "a" "c" "a" "c" "t" "c" "t" "t" "c" "a" "c" "g" "c" "g" "t"
 [73] "t" "c" "c" "t" "g" "g" "g" "t" "c" "a" "t" "g" "t" "a" "t" "g" "t" "g"
 [91] "g" "c" "a" "t" "c" "g" "a" "t" "c" "t"
> s2n(seq)
  [1] 2 1 1 3 2 0 0 1 3 2 3 2 1 1 0 0 2 0 1 2 3 1 1 0 3 1 2 0 0 2 2 0 0 2 3 2 2
 [38] 2 3 2 2 2 0 1 2 1 0 2 0 3 2 2 1 1 2 0 2 0 1 0 1 3 1 3 3 1 0 1 2 1 2 3 3 1
 [75] 1 3 2 2 2 3 1 0 3 2 3 0 3 2 3 2 2 1 0 3 1 2 0 3 1 3
attr(,"levels")
[1] "a" "c" "g" "t"
> #what's happen with unknown characters
> urnmess <- c(urndna,"n")
> seq <- sample( urnmess, 100, replace = TRUE ) ; seq
  [1] "c" "c" "g" "c" "a" "g" "g" "a" "c" "t" "n" "a" "t" "n" "n" "c" "t" "n"
 [19] "n" "c" "c" "a" "c" "g" "n" "g" "c" "a" "g" "n" "c" "a" "c" "t" "c" "t"
 [37] "t" "g" "g" "g" "c" "g" "n" "a" "g" "c" "g" "a" "g" "n" "t" "n" "g" "t"
 [55] "g" "a" "c" "g" "c" "n" "g" "c" "c" "t" "t" "a" "a" "t" "t" "a" "a" "a"
 [73] "c" "a" "c" "a" "c" "a" "g" "t" "a" "g" "n" "c" "a" "a" "c" "a" "a" "c"
 [91] "c" "a" "n" "c" "g" "t" "a" "a" "a" "n"
> s2n(seq)
  [1]  1  1  2  1  0  2  2  0  1  3 NA  0  3 NA NA  1  3 NA NA  1  1  0  1  2 NA
 [26]  2  1  0  2 NA  1  0  1  3  1  3  3  2  2  2  1  2 NA  0  2  1  2  0  2 NA
 [51]  3 NA  2  3  2  0  1  2  1 NA  2  1  1  3  3  0  0  3  3  0  0  0  1  0  1
 [76]  0  1  0  2  3  0  2 NA  1  0  0  1  0  0  1  1  0 NA  1  2  3  0  0  0 NA
attr(,"levels")
[1] "a" "c" "g" "t"
> #How to change the encoding for unknown characters
> tmp <- s2n(seq) ; tmp[is.na(tmp)] <- -1; tmp
  [1]  1  1  2  1  0  2  2  0  1  3 -1  0  3 -1 -1  1  3 -1 -1  1  1  0  1  2 -1
 [26]  2  1  0  2 -1  1  0  1  3  1  3  3  2  2  2  1  2 -1  0  2  1  2  0  2 -1
 [51]  3 -1  2  3  2  0  1  2  1 -1  2  1  1  3  3  0  0  3  3  0  0  0  1  0  1
 [76]  0  1  0  2  3  0  2 -1  1  0  0  1  0  0  1  1  0 -1  1  2  3  0  0  0 -1
attr(,"levels")
[1] "a" "c" "g" "t"
> 
> 
> 
> cleanEx(); ..nameEx <- "splitseq"
> 
> ### * splitseq
> 
> flush(stderr()); flush(stdout())
> 
> ### Name: splitseq
> ### Title: split a sequence into sub-sequences
> ### Aliases: splitseq
> ### Keywords: manip
> 
> ### ** Examples
> 
> a=s2c("aacgttgcaggtcgctcgctacgtagctactgttt")
> ## To obtain the codon sequence in frame 0:
> splitseq(a)
 [1] "aac" "gtt" "gca" "ggt" "cgc" "tcg" "cta" "cgt" "agc" "tac" "tgt"
> 
> 
> 
> cleanEx(); ..nameEx <- "tablecode"
> 
> ### * tablecode
> 
> flush(stderr()); flush(stdout())
> 
> ### Name: tablecode
> ### Title: to plot genetic code as in textbooks
> ### Aliases: tablecode
> ### Keywords: utilities
> 
> ### ** Examples
> 
>  tablecode()
> 
> 
> 
> cleanEx(); ..nameEx <- "translate"
> 
> ### * translate
> 
> flush(stderr()); flush(stdout())
> 
> ### Name: translate
> ### Title: Translate nucleic acid sequences
> ### Aliases: translate
> ### Keywords: manip
> 
> ### ** Examples
> 
> a=read.fasta(File=system.file("sequences/malM.fasta",package ="seqinr"))
> translate(a[[1]])
  [1] "M" "K" "M" "N" "K" "S" "L" "I" "V" "L" "C" "L" "S" "A" "G" "L" "L" "A"
 [19] "S" "A" "P" "G" "I" "S" "L" "A" "D" "V" "N" "Y" "V" "P" "Q" "N" "T" "S"
 [37] "D" "A" "P" "A" "I" "P" "S" "A" "A" "L" "Q" "Q" "L" "T" "W" "T" "P" "V"
 [55] "D" "Q" "S" "K" "T" "Q" "T" "T" "Q" "L" "A" "T" "G" "G" "Q" "Q" "L" "N"
 [73] "V" "P" "G" "I" "S" "G" "P" "V" "A" "A" "Y" "S" "V" "P" "A" "N" "I" "G"
 [91] "E" "L" "T" "L" "T" "L" "T" "S" "E" "V" "N" "K" "Q" "T" "S" "V" "F" "A"
[109] "P" "N" "V" "L" "I" "L" "D" "Q" "N" "M" "T" "P" "S" "A" "F" "F" "P" "S"
[127] "S" "Y" "F" "T" "Y" "Q" "E" "P" "G" "V" "M" "S" "A" "D" "R" "L" "E" "G"
[145] "V" "M" "R" "L" "T" "P" "A" "L" "G" "Q" "Q" "K" "L" "Y" "V" "L" "V" "F"
[163] "T" "T" "E" "K" "D" "L" "Q" "Q" "T" "T" "Q" "L" "L" "D" "P" "A" "K" "A"
[181] "Y" "A" "K" "G" "V" "G" "N" "S" "I" "P" "D" "I" "P" "D" "P" "V" "A" "R"
[199] "H" "T" "T" "D" "G" "L" "L" "K" "L" "K" "V" "K" "T" "N" "S" "S" "S" "S"
[217] "V" "L" "V" "G" "P" "L" "F" "G" "S" "S" "A" "P" "A" "P" "V" "T" "V" "G"
[235] "N" "T" "A" "A" "P" "A" "V" "A" "A" "P" "A" "P" "A" "P" "V" "K" "K" "S"
[253] "E" "P" "M" "L" "N" "D" "T" "E" "S" "Y" "F" "N" "T" "A" "I" "K" "N" "A"
[271] "V" "A" "K" "G" "D" "V" "D" "K" "A" "L" "K" "L" "L" "D" "E" "A" "E" "R"
[289] "L" "G" "S" "T" "S" "A" "R" "S" "T" "F" "I" "S" "S" "V" "K" "G" "K" "G"
[307] "*"
> translate(a[[1]],3,"R",6)
  [1] "P" "L" "A" "F" "Y" "T" "A" "D" "K" "G" "G" "T" "G" "R" "C" "R" "S" "Q"
 [19] "A" "F" "S" "F" "I" "K" "Q" "F" "Q" "R" "L" "I" "N" "I" "T" "F" "R" "D"
 [37] "S" "V" "F" "D" "R" "G" "I" "K" "I" "T" "F" "R" "V" "V" "E" "H" "R" "L"
 [55] "A" "F" "L" "H" "R" "C" "R" "S" "G" "C" "S" "H" "S" "W" "C" "R" "R" "V"
 [73] "T" "Y" "R" "N" "R" "S" "W" "S" "G" "G" "T" "K" "Q" "G" "S" "Y" "Q" "H"
 [91] "A" "G" "A" "G" "V" "R" "F" "H" "F" "Q" "F" "Q" "Q" "A" "I" "G" "G" "M"
[109] "T" "S" "N" "R" "I" "G" "D" "I" "R" "D" "R" "V" "T" "D" "A" "L" "G" "I"
[127] "G" "F" "S" "R" "V" "E" "Q" "L" "G" "R" "L" "L" "E" "I" "F" "F" "R" "G"
[145] "K" "D" "Q" "N" "I" "K" "F" "L" "L" "P" "Q" "R" "R" "C" "Q" "A" "H" "N"
[163] "A" "F" "Q" "P" "I" "C" "T" "H" "H" "A" "W" "F" "L" "V" "G" "E" "I" "T"
[181] "A" "G" "E" "E" "G" "*" "W" "G" "H" "V" "L" "I" "K" "N" "Q" "H" "V" "R"
[199] "R" "K" "N" "A" "G" "L" "F" "V" "H" "F" "A" "G" "Q" "R" "Q" "G" "Q" "F"
[217] "A" "N" "V" "C" "R" "D" "A" "V" "R" "S" "N" "R" "T" "T" "D" "A" "G" "N"
[235] "V" "Q" "L" "L" "A" "A" "G" "R" "Q" "L" "G" "G" "L" "G" "F" "R" "L" "I"
[253] "D" "R" "C" "P" "G" "E" "L" "L" "Q" "R" "S" "R" "W" "N" "G" "W" "R" "V"
[271] "A" "G" "V" "L" "R" "Y" "V" "V" "N" "I" "G" "K" "A" "N" "S" "R" "R" "A"
[289] "C" "Q" "Q" "P" "C" "*" "Q" "T" "E" "D" "D" "E" "T" "F" "I" "H" "F" "H"
> 
> 
> 
> cleanEx(); ..nameEx <- "uco"
> 
> ### * uco
> 
> flush(stderr()); flush(stdout())
> 
> ### Name: uco
> ### Title: Create codon usage table
> ### Aliases: uco
> ### Keywords: manip
> 
> ### ** Examples
> 
> s = read.fasta(File=system.file("sequences/malM.fasta",package = "seqinr"))
> uco( s[[1]], index="freq")

        aaa         aac         aag         aat         aca         acc 
0.048859935 0.039087948 0.013029316 0.006514658 0.009771987 0.055374593 
        acg         act         aga         agc         agg         agt 
0.022801303 0.000000000 0.000000000 0.035830619 0.000000000 0.019543974 
        ata         atc         atg         att         caa         cac 
0.000000000 0.019543974 0.019543974 0.013029316 0.032573290 0.000000000 
        cag         cat         cca         ccc         ccg         cct 
0.019543974 0.003257329 0.019543974 0.016286645 0.042345277 0.003257329 
        cga         cgc         cgg         cgt         cta         ctc 
0.000000000 0.006514658 0.003257329 0.006514658 0.000000000 0.019543974 
        ctg         ctt         gaa         gac         gag         gat 
0.048859935 0.013029316 0.026058632 0.009771987 0.003257329 0.035830619 
        gca         gcc         gcg         gct         gga         ggc 
0.022801303 0.019543974 0.035830619 0.035830619 0.009771987 0.029315961 
        ggg         ggt         gta         gtc         gtg         gtt 
0.009771987 0.016286645 0.013029316 0.019543974 0.022801303 0.029315961 
        taa         tac         tag         tat         tca         tcc 
0.003257329 0.009771987 0.000000000 0.013029316 0.006514658 0.016286645 
        tcg         tct         tga         tgc         tgg         tgt 
0.006514658 0.009771987 0.000000000 0.000000000 0.003257329 0.003257329 
        tta         ttc         ttg         ttt 
0.016286645 0.009771987 0.009771987 0.016286645 
> uco( s[[1]], index="eff")

aaa aac aag aat aca acc acg act aga agc agg agt ata atc atg att caa cac cag cat 
 15  12   4   2   3  17   7   0   0  11   0   6   0   6   6   4  10   0   6   1 
cca ccc ccg cct cga cgc cgg cgt cta ctc ctg ctt gaa gac gag gat gca gcc gcg gct 
  6   5  13   1   0   2   1   2   0   6  15   4   8   3   1  11   7   6  11  11 
gga ggc ggg ggt gta gtc gtg gtt taa tac tag tat tca tcc tcg tct tga tgc tgg tgt 
  3   9   3   5   4   6   7   9   1   3   0   4   2   5   2   3   0   0   1   1 
tta ttc ttg ttt 
  5   3   3   5 
> uco( s[[1]], index="rscu")
      aaa       aac       aag       aat       aca       acc       acg       act 
1.5789474 1.7142857 0.4210526 0.2857143 0.4444444 2.5185185 1.0370370 0.0000000 
      aga       agc       agg       agt       ata       atc       atg       att 
0.0000000 2.2758621 0.0000000 1.2413793 0.0000000 1.8000000 1.0000000 1.2000000 
      caa       cac       cag       cat       cca       ccc       ccg       cct 
1.2500000 0.0000000 0.7500000 2.0000000 0.9600000 0.8000000 2.0800000 0.1600000 
      cga       cgc       cgg       cgt       cta       ctc       ctg       ctt 
0.0000000 2.4000000 1.2000000 2.4000000 0.0000000 1.0909091 2.7272727 0.7272727 
      gaa       gac       gag       gat       gca       gcc       gcg       gct 
1.7777778 0.4285714 0.2222222 1.5714286 0.8000000 0.6857143 1.2571429 1.2571429 
      gga       ggc       ggg       ggt       gta       gtc       gtg       gtt 
0.6000000 1.8000000 0.6000000 1.0000000 0.6153846 0.9230769 1.0769231 1.3846154 
      taa       tac       tag       tat       tca       tcc       tcg       tct 
3.0000000 0.8571429 0.0000000 1.1428571 0.4137931 1.0344828 0.4137931 0.6206897 
      tga       tgc       tgg       tgt       tta       ttc       ttg       ttt 
0.0000000 0.0000000 1.0000000 2.0000000 0.9090909 0.7500000 0.5454545 1.2500000 
> uco( s[[1]], as.data.frame = TRUE)
    AA codon eff        freq      RSCU
1  Lys   aaa  15 0.048859935 1.5789474
2  Asn   aac  12 0.039087948 1.7142857
3  Lys   aag   4 0.013029316 0.4210526
4  Asn   aat   2 0.006514658 0.2857143
5  Thr   aca   3 0.009771987 0.4444444
6  Thr   acc  17 0.055374593 2.5185185
7  Thr   acg   7 0.022801303 1.0370370
8  Thr   act   0 0.000000000 0.0000000
9  Arg   aga   0 0.000000000 0.0000000
10 Ser   agc  11 0.035830619 2.2758621
11 Arg   agg   0 0.000000000 0.0000000
12 Ser   agt   6 0.019543974 1.2413793
13 Ile   ata   0 0.000000000 0.0000000
14 Ile   atc   6 0.019543974 1.8000000
15 Met   atg   6 0.019543974 1.0000000
16 Ile   att   4 0.013029316 1.2000000
17 Gln   caa  10 0.032573290 1.2500000
18 His   cac   0 0.000000000 0.0000000
19 Gln   cag   6 0.019543974 0.7500000
20 His   cat   1 0.003257329 2.0000000
21 Pro   cca   6 0.019543974 0.9600000
22 Pro   ccc   5 0.016286645 0.8000000
23 Pro   ccg  13 0.042345277 2.0800000
24 Pro   cct   1 0.003257329 0.1600000
25 Arg   cga   0 0.000000000 0.0000000
26 Arg   cgc   2 0.006514658 2.4000000
27 Arg   cgg   1 0.003257329 1.2000000
28 Arg   cgt   2 0.006514658 2.4000000
29 Leu   cta   0 0.000000000 0.0000000
30 Leu   ctc   6 0.019543974 1.0909091
31 Leu   ctg  15 0.048859935 2.7272727
32 Leu   ctt   4 0.013029316 0.7272727
33 Glu   gaa   8 0.026058632 1.7777778
34 Asp   gac   3 0.009771987 0.4285714
35 Glu   gag   1 0.003257329 0.2222222
36 Asp   gat  11 0.035830619 1.5714286
37 Ala   gca   7 0.022801303 0.8000000
38 Ala   gcc   6 0.019543974 0.6857143
39 Ala   gcg  11 0.035830619 1.2571429
40 Ala   gct  11 0.035830619 1.2571429
41 Gly   gga   3 0.009771987 0.6000000
42 Gly   ggc   9 0.029315961 1.8000000
43 Gly   ggg   3 0.009771987 0.6000000
44 Gly   ggt   5 0.016286645 1.0000000
45 Val   gta   4 0.013029316 0.6153846
46 Val   gtc   6 0.019543974 0.9230769
47 Val   gtg   7 0.022801303 1.0769231
48 Val   gtt   9 0.029315961 1.3846154
49 Stp   taa   1 0.003257329 3.0000000
50 Tyr   tac   3 0.009771987 0.8571429
51 Stp   tag   0 0.000000000 0.0000000
52 Tyr   tat   4 0.013029316 1.1428571
53 Ser   tca   2 0.006514658 0.4137931
54 Ser   tcc   5 0.016286645 1.0344828
55 Ser   tcg   2 0.006514658 0.4137931
56 Ser   tct   3 0.009771987 0.6206897
57 Stp   tga   0 0.000000000 0.0000000
58 Cys   tgc   0 0.000000000 0.0000000
59 Trp   tgg   1 0.003257329 1.0000000
60 Cys   tgt   1 0.003257329 2.0000000
61 Leu   tta   5 0.016286645 0.9090909
62 Phe   ttc   3 0.009771987 0.7500000
63 Leu   ttg   3 0.009771987 0.5454545
64 Phe   ttt   5 0.016286645 1.2500000
> 
> 
> 
> cleanEx(); ..nameEx <- "words"
> 
> ### * words
> 
> flush(stderr()); flush(stdout())
> 
> ### Name: words
> ### Title: To get all words from an alphabet.
> ### Aliases: words
> ### Keywords: utilities
> 
> ### ** Examples
> 
> ## Get all codons
> words()
 [1] "aaa" "aac" "aag" "aat" "aca" "acc" "acg" "act" "aga" "agc" "agg" "agt"
[13] "ata" "atc" "atg" "att" "caa" "cac" "cag" "cat" "cca" "ccc" "ccg" "cct"
[25] "cga" "cgc" "cgg" "cgt" "cta" "ctc" "ctg" "ctt" "gaa" "gac" "gag" "gat"
[37] "gca" "gcc" "gcg" "gct" "gga" "ggc" "ggg" "ggt" "gta" "gtc" "gtg" "gtt"
[49] "taa" "tac" "tag" "tat" "tca" "tcc" "tcg" "tct" "tga" "tgc" "tgg" "tgt"
[61] "tta" "ttc" "ttg" "ttt"
> ## Get all codons with a c g u for bases
> words(alphabet = c("a", "c", "g", "u"))
 [1] "aaa" "aac" "aag" "aau" "aca" "acc" "acg" "acu" "aga" "agc" "agg" "agu"
[13] "aua" "auc" "aug" "auu" "caa" "cac" "cag" "cau" "cca" "ccc" "ccg" "ccu"
[25] "cga" "cgc" "cgg" "cgu" "cua" "cuc" "cug" "cuu" "gaa" "gac" "gag" "gau"
[37] "gca" "gcc" "gcg" "gcu" "gga" "ggc" "ggg" "ggu" "gua" "guc" "gug" "guu"
[49] "uaa" "uac" "uag" "uau" "uca" "ucc" "ucg" "ucu" "uga" "ugc" "ugg" "ugu"
[61] "uua" "uuc" "uug" "uuu"
> ## Get all tetranucleotides
> words(length = 4)
  [1] "aaaa" "aaac" "aaag" "aaat" "aaca" "aacc" "aacg" "aact" "aaga" "aagc"
 [11] "aagg" "aagt" "aata" "aatc" "aatg" "aatt" "acaa" "acac" "acag" "acat"
 [21] "acca" "accc" "accg" "acct" "acga" "acgc" "acgg" "acgt" "acta" "actc"
 [31] "actg" "actt" "agaa" "agac" "agag" "agat" "agca" "agcc" "agcg" "agct"
 [41] "agga" "aggc" "aggg" "aggt" "agta" "agtc" "agtg" "agtt" "ataa" "atac"
 [51] "atag" "atat" "atca" "atcc" "atcg" "atct" "atga" "atgc" "atgg" "atgt"
 [61] "atta" "attc" "attg" "attt" "caaa" "caac" "caag" "caat" "caca" "cacc"
 [71] "cacg" "cact" "caga" "cagc" "cagg" "cagt" "cata" "catc" "catg" "catt"
 [81] "ccaa" "ccac" "ccag" "ccat" "ccca" "cccc" "cccg" "ccct" "ccga" "ccgc"
 [91] "ccgg" "ccgt" "ccta" "cctc" "cctg" "cctt" "cgaa" "cgac" "cgag" "cgat"
[101] "cgca" "cgcc" "cgcg" "cgct" "cgga" "cggc" "cggg" "cggt" "cgta" "cgtc"
[111] "cgtg" "cgtt" "ctaa" "ctac" "ctag" "ctat" "ctca" "ctcc" "ctcg" "ctct"
[121] "ctga" "ctgc" "ctgg" "ctgt" "ctta" "cttc" "cttg" "cttt" "gaaa" "gaac"
[131] "gaag" "gaat" "gaca" "gacc" "gacg" "gact" "gaga" "gagc" "gagg" "gagt"
[141] "gata" "gatc" "gatg" "gatt" "gcaa" "gcac" "gcag" "gcat" "gcca" "gccc"
[151] "gccg" "gcct" "gcga" "gcgc" "gcgg" "gcgt" "gcta" "gctc" "gctg" "gctt"
[161] "ggaa" "ggac" "ggag" "ggat" "ggca" "ggcc" "ggcg" "ggct" "ggga" "gggc"
[171] "gggg" "gggt" "ggta" "ggtc" "ggtg" "ggtt" "gtaa" "gtac" "gtag" "gtat"
[181] "gtca" "gtcc" "gtcg" "gtct" "gtga" "gtgc" "gtgg" "gtgt" "gtta" "gttc"
[191] "gttg" "gttt" "taaa" "taac" "taag" "taat" "taca" "tacc" "tacg" "tact"
[201] "taga" "tagc" "tagg" "tagt" "tata" "tatc" "tatg" "tatt" "tcaa" "tcac"
[211] "tcag" "tcat" "tcca" "tccc" "tccg" "tcct" "tcga" "tcgc" "tcgg" "tcgt"
[221] "tcta" "tctc" "tctg" "tctt" "tgaa" "tgac" "tgag" "tgat" "tgca" "tgcc"
[231] "tgcg" "tgct" "tgga" "tggc" "tggg" "tggt" "tgta" "tgtc" "tgtg" "tgtt"
[241] "ttaa" "ttac" "ttag" "ttat" "ttca" "ttcc" "ttcg" "ttct" "ttga" "ttgc"
[251] "ttgg" "ttgt" "ttta" "tttc" "tttg" "tttt"
> ## Get all dipeptides
> words(length = 2, alphabet = s2c("ACDEFGHIKLMNPQRSTVWY"))
  [1] "AA" "AC" "AD" "AE" "AF" "AG" "AH" "AI" "AK" "AL" "AM" "AN" "AP" "AQ" "AR"
 [16] "AS" "AT" "AV" "AW" "AY" "CA" "CC" "CD" "CE" "CF" "CG" "CH" "CI" "CK" "CL"
 [31] "CM" "CN" "CP" "CQ" "CR" "CS" "CT" "CV" "CW" "CY" "DA" "DC" "DD" "DE" "DF"
 [46] "DG" "DH" "DI" "DK" "DL" "DM" "DN" "DP" "DQ" "DR" "DS" "DT" "DV" "DW" "DY"
 [61] "EA" "EC" "ED" "EE" "EF" "EG" "EH" "EI" "EK" "EL" "EM" "EN" "EP" "EQ" "ER"
 [76] "ES" "ET" "EV" "EW" "EY" "FA" "FC" "FD" "FE" "FF" "FG" "FH" "FI" "FK" "FL"
 [91] "FM" "FN" "FP" "FQ" "FR" "FS" "FT" "FV" "FW" "FY" "GA" "GC" "GD" "GE" "GF"
[106] "GG" "GH" "GI" "GK" "GL" "GM" "GN" "GP" "GQ" "GR" "GS" "GT" "GV" "GW" "GY"
[121] "HA" "HC" "HD" "HE" "HF" "HG" "HH" "HI" "HK" "HL" "HM" "HN" "HP" "HQ" "HR"
[136] "HS" "HT" "HV" "HW" "HY" "IA" "IC" "ID" "IE" "IF" "IG" "IH" "II" "IK" "IL"
[151] "IM" "IN" "IP" "IQ" "IR" "IS" "IT" "IV" "IW" "IY" "KA" "KC" "KD" "KE" "KF"
[166] "KG" "KH" "KI" "KK" "KL" "KM" "KN" "KP" "KQ" "KR" "KS" "KT" "KV" "KW" "KY"
[181] "LA" "LC" "LD" "LE" "LF" "LG" "LH" "LI" "LK" "LL" "LM" "LN" "LP" "LQ" "LR"
[196] "LS" "LT" "LV" "LW" "LY" "MA" "MC" "MD" "ME" "MF" "MG" "MH" "MI" "MK" "ML"
[211] "MM" "MN" "MP" "MQ" "MR" "MS" "MT" "MV" "MW" "MY" "NA" "NC" "ND" "NE" "NF"
[226] "NG" "NH" "NI" "NK" "NL" "NM" "NN" "NP" "NQ" "NR" "NS" "NT" "NV" "NW" "NY"
[241] "PA" "PC" "PD" "PE" "PF" "PG" "PH" "PI" "PK" "PL" "PM" "PN" "PP" "PQ" "PR"
[256] "PS" "PT" "PV" "PW" "PY" "QA" "QC" "QD" "QE" "QF" "QG" "QH" "QI" "QK" "QL"
[271] "QM" "QN" "QP" "QQ" "QR" "QS" "QT" "QV" "QW" "QY" "RA" "RC" "RD" "RE" "RF"
[286] "RG" "RH" "RI" "RK" "RL" "RM" "RN" "RP" "RQ" "RR" "RS" "RT" "RV" "RW" "RY"
[301] "SA" "SC" "SD" "SE" "SF" "SG" "SH" "SI" "SK" "SL" "SM" "SN" "SP" "SQ" "SR"
[316] "SS" "ST" "SV" "SW" "SY" "TA" "TC" "TD" "TE" "TF" "TG" "TH" "TI" "TK" "TL"
[331] "TM" "TN" "TP" "TQ" "TR" "TS" "TT" "TV" "TW" "TY" "VA" "VC" "VD" "VE" "VF"
[346] "VG" "VH" "VI" "VK" "VL" "VM" "VN" "VP" "VQ" "VR" "VS" "VT" "VV" "VW" "VY"
[361] "WA" "WC" "WD" "WE" "WF" "WG" "WH" "WI" "WK" "WL" "WM" "WN" "WP" "WQ" "WR"
[376] "WS" "WT" "WV" "WW" "WY" "YA" "YC" "YD" "YE" "YF" "YG" "YH" "YI" "YK" "YL"
[391] "YM" "YN" "YP" "YQ" "YR" "YS" "YT" "YV" "YW" "YY"
> 
> 
> 
> cleanEx(); ..nameEx <- "words.pos"
> 
> ### * words.pos
> 
> flush(stderr()); flush(stdout())
> 
> ### Name: words.pos
> ### Title: Positions of possibly degenerated motifs within sequences
> ### Aliases: words.pos
> ### Keywords: utilities
> 
> ### ** Examples
> 
> myseq <- "tatagaga"
> words.pos("t", myseq)   # Should be 1 3
[1] 1 3
> words.pos("tag", myseq) # Should be 3
[1] 3
> words.pos("ga", myseq)  # Should be 5 7
[1] 5 7
> # How to specify ambiguous base ? Look for YpR motifs by
> words.pos("[ct][ag]", myseq) # Should be 1 3
[1] 1 3
> 
> 
> 
> ### * <FOOTER>
> ###
> cat("Time elapsed: ", proc.time() - get("ptime", env = .CheckExEnv),"\n")
Time elapsed:  41.04 0.63 41.96 0 0 
> grDevices::dev.off()
null device 
          1 
> ###
> ### Local variables: ***
> ### mode: outline-minor ***
> ### outline-regexp: "\\(> \\)?### [*]+" ***
> ### End: ***
> quit('no')