Retrieve only the best BLAST hit for each query

This function performs a BLAST search between query and subject sequences and returns only the best hit based on the following criteria.

A best blast hit is defined as:

the hit with the smallest e-value
if e-values are identical then the hit with the longest alignment length is chosen

blast_best_hit(
  query,
  subject,
  search_type = "nucleotide_to_nucleotide",
  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 = 10000,
  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.

search_type

type of query and subject sequences that will be compared via BLAST search. Options are:

search_type = "nucleotide_to_nucleotide"
search_type = "nucleotide_to_protein"
search_type = "protein_to_nucleotide"
search_type = "protein_to_protein"

strand

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

strand = "both" (Default): 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 blast-able database that was formatted with makeblastdb (is.subject.db = TRUE).

task

BLAST search task option (depending on the selected search_type). Options are:

search_type = "nucleotide_to_nucleotide"
- 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"
search_type = "nucleotide_to_protein"
- task = "blastx" : Standard nucleotide-protein comparisons (default).
- task = "blastx-fast" : Optimized nucleotide-protein comparisons.
search_type = "protein_to_nucleotide"
- task = "tblastn" : Standard protein-nucleotide comparisons (default).
- task = "tblastn-fast" : Optimized protein-nucleotide comparisons.
search_type = "protein_to_protein"
- 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 = "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_best_test <- blast_best_hit(
                 query   = system.file('seqs/qry_nn.fa', package = 'metablastr'),
                 subject = system.file('seqs/sbj_nn_best_hit.fa', package = 'metablastr'),
                 search_type = "nucleotide_to_nucleotide",
                 output.path = tempdir(),
                 db.import  = FALSE)
                 
 # look at results
 blast_best_test
}

Arguments

See also

Author

Examples