blastAnalysis: BLAST Analysis of PackTYPE Elements

View source: R/blastAnalysis.R

blastAnalysisR 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)


jackgisby/packFinder documentation built on July 19, 2022, 2:25 a.m.