blastAnalysis: BLAST Analysis of PackTYPE Elements
In packFinder: de novo Annotation of Pack-TYPE Transposable Elements

Description Usage Arguments Value Author(s) References See Also Examples

Run BLAST against user-specified databases of non-transposon and transposon-related proteins. Can be used to classify transposons based on their internal sequences.

blastAnalysis(
  packMatches,
  Genome,
  blastPath,
  protDb = NULL,
  autoDb = NULL,
  minE = 0.001,
  blastTask = "blastn-short",
  maxHits = 100,
  threads = 1,
  saveFolder = NULL,
  tirCutoff = 0
)

`packMatches`	A dataframe of potential Pack-TYPE transposable elements, in the format given by `packSearch`. This dataframe is in the format produced by coercing a `link[GenomicRanges:GRanges-class]{GRanges}` object to a dataframe: `data.frame(GRanges)`. Will be saved as a FASTA file for VSEARCH.
`Genome`	A DNAStringSet object containing sequences referred to in `packMatches` (the object originally used to predict the transposons `packSearch`).
`blastPath`	Path to the BLAST+ executable, or name of the BLAST+ application for Linux/MacOS users.
`protDb`	For assigning Pack-TYPE elements. Path to the blast database containing nucleotide or protein sequences to be matched against internal transposon sequences. Can be generated using BLAST+, or with `link{makeBlastDb}`.
`autoDb`	For assigning autonomous elements. Path to the blast database containing nucleotide or protein sequences to be matched against internal transposon sequences. Can be generated using BLAST+, or with `link{makeBlastDb}`.
`minE`	Blast results with e values greater than the specified cutoff will be ignored.
`blastTask`	Type of BLAST+ task, defaults to "blastn-short".
`maxHits`	Maximum hits returned by BLAST+ per query.
`threads`	Allowable number of threads to be utilised by BLAST+.
`saveFolder`	Directory to save BLAST+ results in; defaults to the working directory.
`tirCutoff`	How many bases to ignore at the terminal ends of the transposons to prevent hits to TIR sequences.

No return value; executes BLAST+ to generate hits which are stored in a .blast file in the chosen directory.

Jack Gisby

For further information, see the NCBI BLAST+ application documentation and help pages (https://www.ncbi.nlm.nih.gov/pubmed/20003500?dopt=Citation).

blastAnnotate, readBlast, packBlast

## Not run: 
packMatches <- data(packMatches)
Genome <- data(arabidopsisThalianaRefseq)

blastAnalysis(packMatches, Genome, 
    protDb = "C:/data/TAIR10_CDS", 
    autoDb = "C:/data/TAIR10_transposons", 
    blastPath = "C:/blast/bin/blastn.exe")

## End(Not run)