bio3d (version 2.3-4)

mustang: 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.

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.

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’.

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) 

}
# }