Description Usage Arguments See Also Examples
Generate a BLAST database from FASTA files.
1 2 | makeblasttdb(input_file, input_type = "fasta", dbtype = "nucl", ...,
show_log = TRUE, show_cmd = FALSE)
|
input_file |
Input file/database name. Multiple file/database names can be provided as a character vector. |
input_type |
Type of data specified in input file. One of “fasta”, “blastdb”, “asn1_bin”, or “asn1_txt”. |
dbtype |
Molecule type of target db (“nucl” or “prot”). |
... |
further arguments passed to |
show_log |
print log file. |
show_cmd |
print the command line instead of executing it. |
Other blast functions: blastn
,
blastn_short
, blastn_short
,
dc_megablast
, dc_megablast
,
megablast
, megablast
;
blastp
, blastp_short
,
blastp_short
; blastx
;
qblast
; rpsblast
;
tblastn
; tblastx
1 2 3 4 5 6 7 8 9 | ## Retrieve, for instance, the human reference genome files located at
## ftp.ncbi.nlm.nih.gov/genomes/H_sapiens/Assembled_chromosomes/seq/
## and generate an input file hs_ref.fa by inflating and concatenating
## the hs_ref_*.fa.gz files.
## Not run:
makeblasttdb("hs_ref.fa", input_type = "fasta", dbtype = "nucl",
parse_seqids = TRUE, out = "hs_ref", title = "Human reference assembly, GRCh28")
## End(Not run)
|
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