**170**wrote:

The task I'm trying to achieve is to align several sequences.

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 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

**20**• written 9.2 years ago by Tal Galili •

**170**

I would not attempt to do this in R unless there is already a library for doing so. There are plenty of good stand-alone multiple sequence alignment programs out there - I would just use one of them.

11kPosted at SO, too: https://stackoverflow.com/q/4497747/680068

9.0k