R: Sequence Alignment with MUSCLE

seqaln {bio3d} | R Documentation

## Sequence Alignment with MUSCLE

### Description

Create multiple alignments of amino acid or nucleotide sequences according to the method of Edgar.

### Usage

    seqaln(aln, id=NULL, profile=NULL, exefile="muscle", outfile="aln.fa",
           protein=TRUE, seqgroup=FALSE, refine=FALSE, extra.args="",
           verbose=FALSE, web.args = list())

### Arguments

`aln` | a sequence character matrix, as obtained from `seqbind`, or an alignment list object as obtained from `read.fasta`.
`id` | a vector of sequence names to serve as sequence identifers.
`profile` | a profile alignment of class ‘fasta’ (e.g. obtained from `read.fasta`). The alignment `aln` will be added to the profile.
`exefile` | file path to the ‘MUSCLE’ program on your system (i.e. how is ‘MUSCLE’ invoked). Alternatively, ‘CLUSTALO’ can be used.
`outfile` | name of ‘FASTA’ output file to which alignment should be written.
`protein` | logical, if TRUE the input sequences are assumed to be protein not DNA or RNA.
`seqgroup` | logical, if TRUE similar sequences are grouped together in the output.
`refine` | logical, if TRUE the input sequences are assumed to already be aligned, and only tree dependent refinement is performed.
`extra.args` | a single character string containing extra command line arguments for the alignment program.
`verbose` | logical, if TRUE ‘MUSCLE’ warning and error messages are printed.
`web.args` | a ‘list’ object containing arguments to perform online sequence alignment using EMBL-EBI Web Services. See below for details.

### Details

Sequence alignment attempts to arrange the sequences of protein, DNA or RNA, to highlight regions of shared similarity that may reflect functional, structural, and/or evolutionary relationships between the sequences.

Aligned sequences are represented as rows within a matrix. Gaps (‘-’) are inserted between the aminoacids or nucleotides so that equivalent characters are positioned in the same column.

This function calls the ‘MUSCLE’ program to perform a multiple sequence alignment, which must be installed on your system and in the search path for executables. If local ‘MUSCLE’ can not be found, alignment can still be performed via online web services (see below) with limited features.

If you have a large number of input sequences (a few thousand), or they are very long, the default settings may be too slow for practical use. A good compromise between speed and accuracy is to run just the first two iterations of the ‘MUSCLE’ algorithm by setting the `extra.args` argument to “-maxiters 2”.

You can set ‘MUSCLE’ to improve an existing alignment by setting `refine` to TRUE.

To inspect the sequence clustering used by ‘MUSCLE’ to produce alignments, include “-tree2 tree.out” in the `extra.args` argument. You can then load the “tree.out” file with the ‘read.tree’ function from the ‘ape’ package.

‘CLUSTALO’ can be used as an alternative to ‘MUSCLE’ by specifiying `exefile='clustalo'`. This might be useful e.g. when adding several sequences to a profile alignment.

If local ‘MUSCLE’ or ‘CLUSTALO’ program is unavailable, the function will attempt to perform alignment via the EMBL-EBI Web Services (See http://www.ebi.ac.uk). In this case, the argument `web.args` cannot be empty and must contain at least user's E-Mail address. Note that as stated by EBI, a fake email address may result in your jobs being killed and your IP, organisation or entire domain being black-listed (See http://www.ebi.ac.uk/Tools/webservices/help/faq). Possible parameters to be passed via `web.args` include:

email

  a string containing a valid E-Mail address. Required.

title

  a string for the title of the job to be submitted to the remote server. Optional.

timeout

  integer specifying the number of seconds to wait for the response of the server before a time out occurs. Default: 90.

An example of usage is `web.args=list(email='user_id@email.provider')`.

### Value

Returns a list of class `"fasta"` with the following components:

`ali` | an alignment character matrix with a row per sequence and a column per equivalent aminoacid/nucleotide.
`id` | sequence names as identifers.
`call` | the matched call.

### Note

A system call is made to the ‘MUSCLE’ program, which must be installed on your system and in the search path for executables. See http://thegrantlab.org/bio3d/tutorials/installing-bio3d for instructions of how to install this program.

### Author(s)

Barry Grant

### References

Grant, B.J. et al. (2006) Bioinformatics 22, 2695–2696.

‘MUSCLE’ is the work of Edgar: Edgar (2004) Nuc. Acid. Res. 32, 1792–1797.

Full details of the ‘MUSCLE’ algorithm, along with download and installation instructions can be obtained from:
http://www.drive5.com/muscle.

### See Also

`read.fasta`, `read.fasta.pdb`, `get.seq`, `seqbind`, `pdbaln`, `plot.fasta`, `blast.pdb`

### Examples

    ## Not run:
    ##-- Basic sequence alignemnt
    seqs <- get.seq(c("4q21_A", "1ftn_A"))
    aln <- seqaln(seqs)

    ##-- add a sequence to the (profile) alignment
    seq <- get.seq("1tnd_A")
    aln <- seqaln(seq, profile=aln)

    ##-- Read a folder/directory of PDB files
    #pdb.path <- "my_dir_of_pdbs"
    #files  <- list.files(path=pdb.path ,
    #                     pattern=".pdb",
    #                     full.names=TRUE)

    ##-- Use online files
    files <- get.pdb(c("4q21","1ftn"), URLonly=TRUE)

    ##-- Extract and store sequences
    raw <- NULL
    for(i in 1:length(files)) {
      pdb <- read.pdb(files[i])
      raw <- seqbind(raw, pdbseq(pdb) )
    }

    ##-- Align these sequences
    aln <- seqaln(raw, id=files, outfile="seqaln.fa")

    ##-- Read Aligned PDBs storing coordinate data
    pdbs <- read.fasta.pdb(aln)

    ## Sequence identity
    seqidentity(aln)

    ## Note that all the above can be done with the pdbaln() function:
    #pdbs <- pdbaln(files)

    ##-- For identical sequences with masking use a custom matrix
    aa <- seqbind(c("X","C","X","X","A","G","K"),
                  c("C","-","A","X","G","X","X","K"))

    aln <- seqaln(aln=aln, id=c("a","b"), outfile="temp.fas", protein=TRUE,
                   extra.args= paste("-matrix",
                    system.file("matrices/custom.mat", package="bio3d"),
                    "-gapopen -3.0 ",
                    "-gapextend -0.5",
                    "-center 0.0") )

    ## End(Not run)

[Package bio3d version 2.3-4 Index]