ClustalW: ClustalW alignment

In rPlant: Interface to the Agave API

Description

An approach for performing multiple alignments of large numbers of amino acid or nucleotide sequences is described. The method is based on first deriving a phylogenetic tree from a matrix of all pairwise sequence similarity scores, obtained using a fast pairwise alignment algorithm. See details on http://www.clustal.org/clustal2/.

Usage

ClustalW(file.name, file.path="", type="DNA", aln.filetype="CLUSTALW", 
         args=NULL, out.name=NULL, job.name=NULL, print.curl=FALSE,   
         shared.username=NULL, suppress.Warnings=FALSE)

Arguments

file.name	Name of file to be evaluated on the Discovery Environment (DE), see details for supported input formats.
file.path	Optional path to a user's subdirectory on the DE; default path is empty, which leads to the home directory
type	Two options "PROTEIN" or "DNA". This defines the type of sequences in the file
aln.filetype	ClustalW does alignment of sequences, this option selects the file type of that result file. There are seven options CLUSTALW, FASTA, PHYLIP_INT, NEXUS, GCG, GDE, and PIR
args	Optional for arguments (i.e. flags). The ClustalW model has much additional functionality that is not fit into this wrapper function (http://www.clustal.org/download/clustalw_help.txt), see details. This option allows users to add anything that is not included (.i.e. args="-ITERATION=TREE"), to iterate at each step, see details.
out.name	The name given to the output filename
job.name	The name to give the job being submitted
print.curl	Prints the curl statement that can be used in the terminal, if curl is installed on your computer
shared.username	With iPlant you have the ability to share folders with other users. If someone has shared a folder with you and you want to run a job with them, enter their username for this input.
suppress.Warnings	This will turn off the warnings, will speed up run time. Use with caution, if the inputs are incorrect they will not be caught.

Details

The supported input file format is the fasta format http://en.wikipedia.org/wiki/FASTA_format.

Additional arguments, args, can be found at http://www.clustal.org/download/clustalw_help.txt. The args input is text with the flags and inputs for those flags in a string like on the command line.

There are seven options for output files: CLUSTALW http://meme.nbcr.net/meme/doc/clustalw-format.html, FASTA http://www.bioperl.org/wiki/PHYLIP_multiple_alignment_format, PHYLIP_INT http://www.bioperl.org/wiki/PHYLIP_multiple_alignment_format, NEXUS http://en.wikipedia.org/wiki/Nexus_file, GCG http://www.genomatix.de/online_help/help/sequence_formats.html#GCG, GDE http://www.cse.unsw.edu.au/~binftools/birch/GDE/overview/GDE.file_formats.html, and PIR http://www.bioinformatics.nl/tools/crab_pir.html.

The result file is ALWAYS ‘clustalw2.fa’.

Value

A list containing the job id and the job name is provided for jobs submitted. If an error, then a message stating the error should also be reported.

See Also

SubmitJob, Validate, UploadFile

Examples

## Not run: data(DNA.fasta)
## Not run: write.fasta(sequences = DNA.fasta, names = names(DNA.fasta), file.out = "DNA.fasta")
## Not run: Validate("username","password")
## Not run: UploadFile("DNA.fasta", filetype="FASTA-0")
## Not run: ClustalW("DNA.fasta", job.name="ClustalWPHY", aln.filetype="PHYLIP_INT")

Example output

Loading required package: rjson
Loading required package: RCurl
Loading required package: bitops
Loading required package: seqinr

rPlant documentation built on April 14, 2017, 6:03 p.m.