Hello everyone,

I am not sure if this should go on the general R mailing list (for example,
if there is a text mining solution that might work here) or the bioconductor
mailing list (since I wasn't able to find a solution to my question on
searching their lists) - so this time I tried both, and in the future I'll
know better (in case it should go to only one of the two).


The task I'm trying to achieve is to align several sequences together.
I don't have a basic pattern to match to.  All that I know is that the
"True" pattern should be of length "30" and that the sequences I'm looking
at, have had missing values introduced to them at random points.
Here is an example of such sequences, were on the left we see what is the
real location of the missing values, and on the right we see the sequence
that we will be able to observe.  My goal is to reconstruct the left column
using only the sequences I've got on the right column (based on the fact
that many of the letters in each position are the same)

                     Real_sequence           The_sequence_we_see

1   CGCAATACTAAC-AGCTGACTTACGCACCG CGCAATACTAACAGCTGACTTACGCACCG

2   CGCAATACTAGC-AGGTGACTTCC-CT-CG   CGCAATACTAGCAGGTGACTTCCCTCG

3   CGCAATGATCAC--GGTGGCTCCCGGTGCG  CGCAATGATCACGGTGGCTCCCGGTGCG

4   CGCAATACTAACCA-CTAACT--CGCTGCG   CGCAATACTAACCACTAACTCGCTGCG

5   CGCACGGGTAAGAACGTGA-TTACGCTCAG CGCACGGGTAAGAACGTGATTACGCTCAG

6   CGCTATACTAACAA-GTG-CTTAGGC-CTG   CGCTATACTAACAAGTGCTTAGGCCTG

7   CCCA-C-CTAA-ACGGTGACTTACGCTCCG   CCCACCTAAACGGTGACTTACGCTCCG


Here is an example code to reproduce the above example:

ATCG <- c("A","T","C","G")

set.seed(40)


original.seq <- sample(ATCG, 30, T)


seqS <- matrix(original.seq,200,30, T)


change.letters <- function(x, number.of.changes = 15,
letters.to.change.with = ATCG)

{


    number.of.changes <- sample(seq_len(number.of.changes), 1)


    new.letters <- sample(letters.to.change.with , number.of.changes, T)


    where.to.change.the.letters <- sample(seq_along(x) , number.of.changes, F)


    x[where.to.change.the.letters] <- new.letters


    return(x)

}


change.letters(original.seq)


insert.missing.values <- function(x) change.letters(x, 3, "-")


insert.missing.values(original.seq)


seqS2 <- t(apply(seqS, 1, change.letters))


seqS3 <- t(apply(seqS2, 1, insert.missing.values))


seqS4 <- apply(seqS3,1, function(x) {paste(x, collapse = "")})

require(stringr)

# library(help=stringr)


all.seqS <- str_replace(seqS4,"-" , "")


# how do we allign this?


data.frame(Real_sequence = seqS4, The_sequence_we_see = all.seqS)


I understand that if all I had was a string and a pattern I would be able to
use

library(Biostrings)


pairwiseAlignment(...)



But in the case I present we are dealing with many sequences to align to one
another (instead of aligning them to one pattern).

Is there a known method for doing this in R?


Thanks,

Tal



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