blastTranscriptomes: BLAST search local transcriptomes

In thebustalab/phylochemistry: Chemical and Sequence Analyses in a Phylogenetic Context

Description

Search locally stored transcriptomes for query sequences.

Usage

blastTranscriptomes(
  transcriptomes,
  initial_query_in_path,
  iterative_blast = FALSE,
  iterative_blast_length_cutoff = 700,
  sequences_of_interest_directory_path,
  blast_module_directory_path,
  blast_type = c("blastn", "dc-megablast"),
  remove = NULL,
  monolist_out_path
)

Arguments

transcriptomes	A list of paths to the transcriptomes that should be searched, named by taxonomic identifier (e.g. species names)
initial_query_in_path	Path to a fasta file containing the query
sequences_of_interest_directory_path	Path to a directory where blast hits should be written out as fasta files
blast_module_directory_path	Path to directory containing the BLAST+ module (perhaps something like "/usr/local/ncbi/blast/bin/")
blast_type	One of "blastn" or "dc-megablast". "blastn" is a traditional BLASTN requiring an exact match of 11. "dc-megablast" is a discontiguous megablast used to find more distant (e.g., interspecies) sequences.
remove	Names of columns to remove from the output monolist
monolist_out_path	Path to where the output monolist should be written

thebustalab/phylochemistry documentation built on Sept. 3, 2021, 5:06 a.m.