blastAnalysis {packFinder} | R Documentation

## BLAST Analysis of PackTYPE Elements

### Description

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

### Usage

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

### Arguments

`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.

### Value

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

### Author(s)

Jack Gisby

### References

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

### See Also

`blastAnnotate`, `readBlast`, `packBlast`

### Examples

    ## 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)

[Package packFinder version 1.0.0 Index]