Description Usage Arguments Value Examples
NCBI BLAST (Basic Local Alignment Search Tool)
1 |
query |
either a string pointing to the query file, an object of class DNAbin, or an object of class XStringSet |
db |
string pointing to the BLAST database, or if the switch 'remote' is provided in 'args', the name of the remote NCBI database |
args |
A named list containing the BLAST program arguments to be used in a key/value manner. There is no need to use leading dashes on the argument names. SEE EXAMPLES |
type |
string with the name of the BLAST program to use. e.g. 'blastp' or 'blastn' |
gz |
boolean. For gzip'd query files. if 'TRUE', the query file is uncompressed and read stdin into the BLAST program |
An object of class 'data.table'. Only format '6' (tabular format) for 'outfmt' is supported.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 | ##Run local primer blast
query <- readDNAStringSet("ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/010/525/GCA_000010525.1_ASM1052v1/GCA_000010525.1_ASM1052v1_genomic.fna.gz")
primers <- c("GGCTGGATCACCTCCTT","GCCWAGGCATCCDCC")
db <- makeprimerdb(primers)
#Define BLAST arguments: these are the same that can be found in `RinsilicoPCR::blast.params$primers`
args <- list(
outfmt="'6 qacc sacc pident length qlen slen qstart sstart qend send evalue'",
max_target_seqs=20,
word_size=8
)
blastres <- blast(query,db,args)
##Run remote blast on NCBI blastdb `nt`
query <- readDNAStringSet("query.fa")
#Define BLAST arguments: these are the same that can be found in `RinsilicoPCR::blast.params$remote`
args <- list(
outfmt="'6 qacc sacc pident length qlen slen qstart sstart qend send evalue'",
max_target_seqs=20,
word_size=11,
remote=""
)
blastres <- blast(query,db="nt",args)
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