This function takes a fasta file containing query sequences as input and performs BLAST searches of these query sequences against a set of reference genomes to retrieve corresponding hits in diverse genomes.
blast_nucleotide_to_genomes( query, subject_genomes, blast_type = "blastn", blast_output_path = "blast_output", min_alig_length = 30, evalue = 1e-05, max.target.seqs = 5000, update = FALSE, ... )
path to input file in fasta format.
a vector containing file paths to the reference genomes that shall be queried (e.g. file paths returned by
specification of the BLAST type shall be used to perform BLAST searches between query and reference. Available options are:
a path to a folder that will be created to store BLAST output tables for each individual query-genome search.
minimum alignment length that shall be retained in the result dataset. All hit alignments with smaller hit alignment length will be removed automatically.
minimum expectation value (E) threshold for retaining hits (default: evalue = 0.00001).
maximum number of aligned sequences that shall be retained. Please be aware that
a logical value indicating whether or not pre-computed BLAST tables should be removed and re-computed (
blast_nucleotide_to_genomes function enables users to BLAST specific query sequences against a set of reference genomes
and retrieve the corresponding BLAST output.