Complement a DNA sequence

user_1734049 0
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Suppose I have a DNA sequence. I want to get the complement of it. I used the following code but I am not getting it. What am I doing wrong ?

s=readline()
ATCTCGGCGCGCATCGCGTACGCTACTAGC
p=unlist(strsplit(s,""))
h=rep("N",nchar(s))
unlist(lapply(p,function(d){
for b in (1:nchar(s)) {    
    if (p[b]=="A") h[b]="T"
    if (p[b]=="T") h[b]="A"
    if (p[b]=="G") h[b]="C"
    if (p[b]=="C") h[b]="G"
}
genetics bioinformatics complement r replace
7 Answers

Use chartr which is built for this purpose:

> s
[1] "ATCTCGGCGCGCATCGCGTACGCTACTAGC"
> chartr("ATGC","TACG",s)
[1] "TAGAGCCGCGCGTAGCGCATGCGATGATCG"

Just give it two equal-length character strings and your string. Also vectorised over the argument for translation:

> chartr("ATGC","TACG",c("AAAACG","TTTTT"))
[1] "TTTTGC" "AAAAA"

Note I'm doing the replacement on the string representation of the DNA rather than the vector. To convert the vector I'd create a lookup-map as a named vector and index that:

> p
 [1] "A" "T" "C" "T" "C" "G" "G" "C" "G" "C" "G" "C" "A" "T" "C" "G" "C" "G" "T"
[20] "A" "C" "G" "C" "T" "A" "C" "T" "A" "G" "C"
> map=c("A"="T", "T"="A","G"="C","C"="G")
> unname(map[p])
 [1] "T" "A" "G" "A" "G" "C" "C" "G" "C" "G" "C" "G" "T" "A" "G" "C" "G" "C" "A"
[20] "T" "G" "C" "G" "A" "T" "G" "A" "T" "C" "G"
user_2111160

The Bioconductor package Biostrings has many useful functions for this sort of operation. Install once:

source("http://bioconductor.org/biocLite.R")
biocLite("Biostrings")

then use

library(Biostrings)
dna = DNAStringSet(c("ATCTCGGCGCGCATCGCGTACGCTACTAGC", "ACCGCTA"))
complement(dna)
user_5473310 
sapply(p, switch,  "A"="T", "T"="A","G"="C","C"="G")
  A   T   C   T   C   G   G   C   G   C   G   C   A   T   C   G   C   G   T 
"T" "A" "G" "A" "G" "C" "C" "G" "C" "G" "C" "G" "T" "A" "G" "C" "G" "C" "A" 
  A   C   G   C   T   A   C   T   A   G   C 
"T" "G" "C" "G" "A" "T" "G" "A" "T" "C" "G"

If you do not want the complementary names, you can always strip them with unname.

unname(sapply(p, switch,  "A"="T", "T"="A","G"="C","C"="G") )
 [1] "T" "A" "G" "A" "G" "C" "C" "G" "C" "G" "C" "G" "T" "A" "G" "C" "G" "C"
[19] "A" "T" "G" "C" "G" "A" "T" "G" "A" "T" "C" "G"
>
user_18556770

Here a answer using base r. Written with a horrible formatting to make things clear and to keep it as a one-liner. It supports upper and lower cases.

revc = function(s){
       paste0(
           rev(
            unlist(
             strsplit(
                chartr("ATGCatgc","TACGtacg",s)
                      , "")                        # from strsplit
                   )                               # from unlist
               )                                   # from rev
             , collapse='')                        # from paste0
       }
user_4890100

I've generalised the solution rev(comp(seq)) with the seqinr package:

install.packages("devtools")
devtools::install_github("TomKellyGenetics/tktools")
tktools::revcomp(seq)

This version is compatible with string inputs and is vectorised to handle list or vector input of multiple strings. The output class should match the input, including cases and types. This also support inputs containing "U" for RNA and RNA output sequences.

> seq <- "ATCTCGGCGCGCATCGCGTACGCTACTAGC"
> revcomp(seq)
[1] "GCTAGTAGCGTACGCGATGCGCGCCGAGAT"

> seq <- c("TATAAT", "TTTCGC", "atgcat")
> revcomp(seq)
  TATAAT   TTTCGC   atgcat 
 "ATTATA" "GCGAAA" "atgcat"

See the manual or the TomKellyGenetics/tktools github package repository.

user_42166250
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