R mismatch position in pairwise alignment

[NicoBxl]

Hi everybody,

I've a little question. In R, I've two sequences ( DNA sequences ) and I want to align them and known the mismatch positions.

For example :

seq1 <- "ATGC"
seq2 <- "ATGG"

mismatch.pos <- aCoolFunction(seq1,seq2)

mismatch.pos
--> 4

Anyone knows such thing ?

if it doesn't exist in R, is it easily possible in bioperl ?

[dariober]

What about...

x <- "ATGCGACTG"
y <- "ATGGNACTG"

seqdiff<- function(seq1, seq2){
    seq<- strsplit(c(seq1, seq2), split= '')
    mismatches<- which(seq[[1]] != seq[[2]])
    return(mismatches)
    }

seqdiff(x, y)
--> [1] 4 5

(Note: No attempt is made to cope with sequences of different length, which() will throw a warning in such case).

Dario

[NicoBxl]

thanks but in most of the cases the sequences have different length

[dariober]

...The variant below will right-pad the shorter sequence with 'X', which in turn will be considered as differences (not sure this is what you want...)

I assume that your sequences have been already aligned by some other program and what you want is to pull out the mismatches.

If instead you really want to do sequence alignment within R, I accidentally found the package bio3d which has a function called seqaln, see if it helps.

Anyway, I think R is not ideal for such jobs, I'd rather go for python or perl after BLAST or other aligner.

Dario

seqdiff<- function(seq1, seq2){
    seq<- strsplit(c(seq1, seq2), split= '')

    ## If the length of the two sequences differs, 
    ## pad the shorter one with X
    seqlen<- length(seq[[1]]) - length(seq[[2]])
    if(seqlen > 0){
        seq[[2]]<- append(seq[[2]], rep('X', seqlen))
        }
    if(seqlen < 0){
        seq[[1]]<- append(seq[[1]], rep('X', abs(seqlen)))
        }

    mismatches<- which(seq[[1]] != seq[[2]])
    return(mismatches)
    }

[svl]

Are you using bioconductor?

This should be doable with bioconductor as well.

How to install bioconductor:
source(“http://www.bioconductor.org/biocLite.R”)
biocLite()

How to create an aligment:

http://manuals.bioinformatics.ucr.edu/home/ht-seq#TOC-Computing-Pairwise-Sequence-Alignme

And here's the alignments vignette/doc:

http://bioconductor.org/packages/2.5/bioc/vignettes/Biostrings/inst/doc/Alignments.pdf

... in this pdf focus on the function: mismatchTable -- Creates a table for the mismatching positions

Seems to be what you want. Let us know if and how you got it to work!

/Stef