View source: R/detect_homologs_cds_to_cds.R
detect_homologs_cds_to_cds | R Documentation |
Run cds to cds BLAST searches to detect homologous cds sequences in a set of subject cds files.
detect_homologs_cds_to_cds(
query,
subject_cds,
task = "blastn",
blast_output_path = "blast_output",
min_alig_length = 60,
evalue = 1e-05,
max.target.seqs = 5000,
cores = 1,
update = FALSE,
...
)
query |
path to input file in fasta format. |
subject_cds |
a character vector containing paths to subject files in fasta format. |
task |
nucleotide search task option. Options are:
|
blast_output_path |
a path to a folder that will be created to store BLAST output tables for each individual query-cds search. |
min_alig_length |
minimum alignment length that shall be retained in the result dataset. All hit alignments with smaller hit alignment length will be removed automatically. |
evalue |
Expectation value (E) threshold for saving hits (default: evalue = 1E-5). |
max.target.seqs |
maximum number of aligned sequences that shall be kept. Default is |
cores |
number of cores for parallel BLAST searches. |
update |
a logical value indicating whether or not pre-computed BLAST tables should be removed and re-computed ( |
... |
additional arguments passed to |
Hajk-Georg Drost
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