bio3d (version 2.1-2)

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", 
       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.

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 sequence alignment, which MUST BE INSTALLED on your system and in the search path for executables.

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

##-- Read a folder/directory of 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)