blast_protein_to_nr_database: Perform Protein to Protein BLAST Searches Against the NCBI NR...

In HajkD/metablastr: Perform Massive Local BLAST Searches

Perform Protein to Protein BLAST Searches Against the NCBI NR Database

Description

Run protein to protein BLAST of reference sequences against the NCBI non-redundant protein sequence Database.

Usage

blast_protein_to_nr_database(
  query,
  nr.database,
  nr.needs.formatting = FALSE,
  output.path = NULL,
  task = "blastp",
  db.import = FALSE,
  postgres.user = NULL,
  evalue = 1e-05,
  out.format = "csv",
  cores = 1,
  max.target.seqs = 65200,
  db.soft.mask = TRUE,
  db.hard.mask = TRUE,
  blast.path = NULL
)

Arguments

query	path to input file in fasta format.
nr.database	path to local NCBI NR database.
nr.needs.formatting	a logical value indicating whether or not the local database specified in nr.database is already pre-formatted (nr.needs.formatting = FALSE; default) or whether the local NCBI NR databasse still requires formatting (nr.needs.formatting = TRUE).
output.path	path to folder at which BLAST output table shall be stored. Default is output.path = NULL (hence getwd() is used).
task	protein search task option. Options are: task = "blastp" : Standard protein-protein comparisons (default). task = "blast-fast" : Improved BLAST searches using longer words for protein seeding. task = "blastp-short" : Optimized protein-protein comparisons for query sequences shorter than 30 residues.
db.import	shall the BLAST output be stored in a PostgresSQL database and shall a connection be established to this database? Default is db.import = FALSE. In case users wish to to only generate a BLAST output file without importing it to the current R session they can specify db.import = NULL.
postgres.user	when db.import = TRUE and out.format = "postgres" is selected, the BLAST output is imported and stored in a PostgresSQL database. In that case, users need to have PostgresSQL installed and initialized on their system. Please consult the Installation Vignette for details.
evalue	Expectation value (E) threshold for saving hits (default: evalue = 0.001).
out.format	a character string specifying the format of the file in which the BLAST results shall be stored. Available options are: out.format = "pair" : Pairwise out.format = "qa.ident" : Query-anchored showing identities out.format = "qa.nonident" : Query-anchored no identities out.format = "fq.ident" : Flat query-anchored showing identities out.format = "fq.nonident" : Flat query-anchored no identities out.format = "xml" : XML out.format = "tab" : Tabular separated file out.format = "tab.comment" : Tabular separated file with comment lines out.format = "ASN.1.text" : Seqalign (Text ASN.1) out.format = "ASN.1.binary" : Seqalign (Binary ASN.1) out.format = "csv" : Comma-separated values out.format = "ASN.1" : BLAST archive (ASN.1) out.format = "json.seq.aln" : Seqalign (JSON) out.format = "json.blast.multi" : Multiple-file BLAST JSON out.format = "xml2.blast.multi" : Multiple-file BLAST XML2 out.format = "json.blast.single" : Single-file BLAST JSON out.format = "xml2.blast.single" : Single-file BLAST XML2 out.format = "report" : Organism Report
cores	number of cores for parallel BLAST searches.
max.target.seqs	maximum number of aligned sequences that shall be retained. Please be aware that max.target.seqs selects best hits based on the database entry and not by the best e-value. See details here: https://academic.oup.com/bioinformatics/advance-article/doi/10.1093/bioinformatics/bty833/5106166 .
db.soft.mask	shall low complexity regions be soft masked? Default is db.soft.mask = FALSE.
db.hard.mask	shall low complexity regions be hard masked? Default is db.hard.mask = FALSE.
blast.path	path to BLAST executables.

Author(s)

Hajk-Georg Drost

See Also

blast_nucleotide_to_nucleotide, blast_nucleotide_to_protein, blast_protein_to_nucleotide, blast_best_hit

Examples

## Not run: 
blast_example <- blast_protein_to_nr_database(
              query   = system.file('seqs/qry_aa.fa', package = 'metablastr'),
              nr.database = "nr",
              output.path = tempdir(),
              db.import  = FALSE)
              
# look at BLAST results
blast_example

## End(Not run)

HajkD/metablastr documentation built on Sept. 14, 2023, 5:26 p.m.