View source: R/blast_protein_to_proteomes.R
blast_protein_to_proteomes | R Documentation |
This function takes a fasta file containing query sequences as input and performs BLAST searches of these query sequences against a set of reference proteomes to retrieve corresponding hits in diverse proteomes
blast_protein_to_proteomes(
query,
subject_proteomes,
blast_type = "blastp",
blast_output_path = "blast_output",
min_alig_length = 30,
evalue = 1e-05,
max.target.seqs = 5000,
update = FALSE,
...
)
query |
path to input file in fasta format. |
subject_proteomes |
a vector containing file paths to the reference proteomes that shall be queried (e.g. file paths returned by |
blast_type |
specification of the BLAST type shall be used to perform BLAST searches between query and reference. Available options are:
|
blast_output_path |
a path to a folder that will be created to store BLAST output tables for each individual query-proteome 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 |
minimum expectation value (E) threshold for retaining hits (default: evalue = 0.00001). |
max.target.seqs |
maximum number of aligned sequences that shall be retained. Please be aware that |
update |
a logical value indicating whether or not pre-computed BLAST tables should be removed and re-computed ( |
... |
additional arguments passed to |
The blast_protein_to_proteomes
function enables users to BLAST specific query sequences against a set of reference proteomes
and retrieve the corresponding BLAST output.
Hajk-Georg Drost
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