Perform Nucleotide to Nucleotide BLAST Searches (BLASTN)

Source: R/blast_nucleotide_to_nucleotide.R

Run nucleotide to nucleotide BLAST of reference sequences against a blast-able database or fasta file.

blast_nucleotide_to_nucleotide(
  query,
  subject,
  strand = "both",
  output.path = NULL,
  is.subject.db = FALSE,
  task = "blastn",
  db.import = FALSE,
  postgres.user = NULL,
  evalue = 0.001,
  out.format = "csv",
  cores = 1,
  max.target.seqs = 10000L,
  db.soft.mask = FALSE,
  db.hard.mask = FALSE,
  blast.path = NULL
)

Arguments

query

path to input file in fasta format.

subject

path to subject file in fasta format or blast-able database.

strand

Query DNA strand(s) to search against database/subject. Options are:

  • strand = "both" : query against both DNA strands.

  • strand = "minus" : query against minus DNA strand.

  • strand = "plus" : query against plus DNA strand.

output.path

path to folder at which BLAST output table shall be stored. Default is output.path = NULL (hence getwd() is used).

is.subject.db

logical specifying whether or not the subject file is a file in fasta format (is.subject.db = FALSE; default) or a fasta file that was previously converted into a blast-able database using makeblastdb (is.subject.db = TRUE).

task

nucleotide search task option. Options are:

  • task = "blastn" : Standard nucleotide-nucleotide comparisons (default) - Traditional BLASTN requiring an exact match of 11.

  • task = "blastn-short" : Optimized nucleotide-nucleotide comparisons for query sequences shorter than 50 nucleotides.

  • task = "dc-megablast" : Discontiguous megablast used to find somewhat distant sequences.

  • task = "megablast" : Traditional megablast used to find very similar (e.g., intraspecies or closely related species) sequences.

  • task = "rmblastn"

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 = "SAM" : Sequence Alignment/Map (SAM)

  • 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

Hajk-Georg Drost

Examples

if (FALSE) {
blast_test <- blast_nucleotide_to_nucleotide(
                 query   = system.file('seqs/qry_nn.fa', package = 'metablastr'),
                 subject = system.file('seqs/sbj_nn.fa', package = 'metablastr'),
                 output.path = tempdir(),
                 db.import  = FALSE)
                 
 # look at results
 blast_test
}