6 Reading frames in R for protein from DNA sequence

Question

[Tanvir Ahamed]

Can any one help to get 6 reading frames in R for protein sequences from DNA sequence?

Thanks

[Tanvir Ahamed]

My solution:

getTrans {seqinr} this command is useful.

Answer 1

[Tanvir Ahamed]

Read a fasta file

library(seqinr) 
fast_file <- read.fasta("E:\\SAS\\Nuc\\t_GCA_000536675.1.fa",as.string = TRUE,seqtype="AA")

Sample header of the fasta file

.>adpmb-supercont1.5 dna:supercontig supercontig:GCA_000536675.1:adpmb-supercont1.5:1:221212:1 CCTTGTTAATTTTTATTTAAAGTAAAATATCCCTTTAATATCTCCTCTTAAACTACTTTA ACTACTATTATTTATTATACTATGGTTAATACATCACCGGATGGATGATTATGAACTGCG ATGATTGCATTGGCATTTTCTCTCACCGCAATACTAAAAATTTCACGTGGATGTACAATC

Input for the function

• contig = Name of sequence in fasta file
• file = Name of fasta formated file
• from = Start of sequence in DNA sequence
• to = Stop of sequence in DNA sequence
• strand = Strand of the sequence

Examples:

res <- cont2nuc(contig="adpmb-supercont1.5",file=fast_t,from=116271,to=122902,strand=1)

Function in R :

- Name : Convert DNA sequence to Protein sequence (6 reading frame)

- R-code

cont2nuc<-function(contig="adpmb-supercont1.5",file=fast,from=116271,to=122902,strand=1)
        {
        require(seqinr)
        fasta<-file[which(contig==names(file))]
        att<-attributes(fasta[[1]])
        att2<-att[[2]]
        sequ<-substr((fasta[[1]][1]),from,to)

        strReverse <- function(x) sapply(lapply(strsplit(x, NULL), rev), paste, collapse="")

        sequ1<-strReverse(sequ)
        contig_strand<-as.numeric(as.character(substr(att2,nchar(att2),nchar(att2))))

        if((contig_strand==strand)==TRUE)
            {
            f1<-paste(getTrans(s2c(sequ),frame=0,sens="F"),collapse = '')
            f1_dna<-sequ
            f2<-paste(getTrans(s2c(sequ),frame=1,sens="F"),collapse = '')
            f2_dna<-substr(sequ,2,nchar(sequ))
            f3<-paste(getTrans(s2c(sequ),frame=2,sens="F"),collapse = '')
            f3_dna<-substr(sequ,3,nchar(sequ))

            r1<-paste(getTrans(s2c(sequ),frame=0,sens="R"),collapse = '')
            r1_dna<-paste(comp(s2c(sequ1),forceToLower = FALSE),collapse = '')
            r2<-paste(getTrans(s2c(sequ),frame=1,sens="R"),collapse = '')
            r2_dna<-paste(comp(s2c(substr(sequ1,2,nchar(sequ1))),forceToLower = FALSE),collapse = '')
            r3<-paste(getTrans(s2c(sequ),frame=2,sens="R"),collapse = '')
            r3_dna<-paste(comp(s2c(substr(sequ1,3,nchar(sequ1))),,forceToLower = FALSE),collapse = '')

            res<-list(f1,f1_dna,f2,f2_dna,f3,f3_dna,r1,r1_dna,r2,r2_dna,r3,r3_dna)
            names(res)<-c("for_1","for_1_DNA","for_2","for_2_DNA","for_3","for_3_DNA","rev_1","rev_1_DNA","rev_2","rev_2_DNA","rev_3","rev_3_DNA")
            return(res)
            #return(list(sequ,sequ1))
            }
        if ((contig_strand==strand)==FALSE)
            {note<-"CHECK"
            return(note)}
        }