R: Structure-based Sequence Alignment with MUSTANG

mustang {bio3d} | R Documentation

## Structure-based Sequence Alignment with MUSTANG

### Description

Create a multiple sequence alignment from a bunch of PDB files.

### Usage

    mustang(files, exefile="mustang", outfile="aln.mustang.fa",
            cleanpdb=FALSE, cleandir="mustangpdbs", verbose=TRUE)

### Arguments

`files` | a character vector of PDB file names.
`exefile` | file path to the ‘MUSTANG’ program on your system (i.e. how is ‘MUSTANG’ invoked).
`outfile` | name of ‘FASTA’ output file to which alignment should be written.
`cleanpdb` | logical, if TRUE iterate over the PDB files and map non-standard residues to standard residues (e.g. SEP->SER..) to produce ‘clean’ PDB files.
`cleandir` | character string specifying the directory in which the ‘clean’ PDB files should be written.
`verbose` | logical, if TRUE ‘MUSTANG’ warning and error messages are printed.

### Details

Structure-based sequence alignment with ‘MUSTANG’ attempts to arrange and align the sequences of proteins based on their 3D structure.

This function calls the ‘MUSTANG’ program, to perform a multiple structure alignment, which MUST BE INSTALLED on your system and in the search path for executables.

Note that non-standard residues are mapped to “Z” in MUSTANG. As a workaround the bio3d ‘mustang’ function will attempt to map any non-standard residues to standard residues (e.g. SEP->SER, etc). To avoid this behaviour use ‘cleanpdb=FALSE’.

### Value

A list with two components:

`ali` | an alignment character matrix with a row per sequence and a column per equivalent aminoacid.
`ids` | sequence names as identifers.

### Note

A system call is made to the ‘MUSTANG’ program, which must be installed on your system and in the search path for executables.

### Author(s)

Lars Skjaerven

### References

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

‘MUSTANG’ is the work of Konagurthu et al: Konagurthu, A.S. et al. (2006) Proteins 64(3):559–74.

More details of the ‘MUSTANG’ algorithm, along with download and installation instructions can be obtained from:
http://www.csse.monash.edu.au/~karun/Site/mustang.html.

### See Also

`read.fasta`, `read.fasta.pdb`, `pdbaln`, `plot.fasta`, `seqaln`

### Examples

    ## Not run:

    if(!check.utility('mustang')) {
       message('Need MUSTANG installed to run this example')
    } else {

    ## Fetch PDB files and split to chain A only PDB files
    ids <- c("1a70_A", "1czp_A", "1frd_A")
    files <- get.pdb(ids, split = TRUE, path = tempdir())

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

    ##-- Align these PDB sequences
    aln <- mustang(files)

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

    }

    ## End(Not run)

[Package bio3d version 2.3-3 Index]