blastr: Execute BLAST from R.

In brouwern/compbio4all: Datasets and helpful functions for learning bioinformatics and computational biology

Description

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.

Usage

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

brouwern/compbio4all documentation built on Dec. 19, 2021, 11:47 a.m.