Execute BLAST from R.

Code is modified from the blast.pdb() function of bio3d to allow different databases to be queried and the maximum number of hits to be changed.

blastr(
  seq,
  program = "blastp",
  database = "refseq_protein",
  time.out = NULL,
  chain.single = TRUE,
  maxhits = 2000
)

Arguments

seq

Sequence as character string, eg "ACVPTY" or "ATCGGC"
program

blastn, blastp, blastx, tblastn, tblastx
database

Defaults to refseq_protein Other options include nt (nucleotide), nr (non-redundant protein), refseq_rna (NCBI Transcript Reference Sequences DNA), swissprot (Non-redundant UniProtKB/SwissProt sequences Protein), pdbaa (PDB protein database), pdbnt (PDB nucleotide database)
time.out

xxx
chain.single

xxxx
maxhits

Maximum number of hits to keep. Passed to BLAST parameter HITLIST_SIZE

Details

For more information see General: https://ncbi.github.io/blast-cloud/dev/api.html Databases: https://ncbi.github.io/blast-cloud/blastdb/available-blastdbs.html for