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Run DELTABLAST to find homologs for proteins of interest

Source: R/blastWrappers.R
runDeltaBlast.Rd

This function executes a Delta-BLAST search using the specified parameters and database. It sets the BLAST database path, runs the Delta-BLAST command with the given query, and outputs the results.

Usage

runDeltaBlast(
  runDeltaBlast,
  db_search_path,
  db = "refseq",
  query,
  evalue = "1e-5",
  out,
  num_alignments,
  num_threads = 1
)

Arguments

db_search_path

Path to the BLAST databases.

db

Name of the BLAST database to search against (default is "refseq").

query

Path to the input query file.

evalue

E-value threshold for reporting matches (default is "1e-5").

out

Path to the output file where results will be saved.

num_alignments

Number of alignments to report.

num_threads

Number of threads to use for the search (default is 1).

deltablast_path

Path to the Delta-BLAST executable.

Value

This function does not return a value; it outputs results to the specified file.

Author

Samuel Chen, Janani Ravi

Examples

if (FALSE) { # \dontrun{
runDeltaBlast(runDeltaBlast, db_search_path)
} # }