blastDbase16S: Building a BLAST database

In microclass: Methods for Taxonomic Classification of Prokaryotes

Description

Building a BLAST database for 16S based classification.

Usage

blastDbase16S(name, sequence, taxon)

Arguments

name	The name of the database (text).
sequence	A character vector with 16S sequence data.
taxon	A character vector with taxon information.

Details

This functions builds a database using the makeblastdb program of the BLAST+ software https://blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE_TYPE=BlastDocs&DOC_TYPE=Download. Thus, this software must be available on the system when using this function. If you type system("makeblastdb -help") in the Console window some meaningful Help-text should be displayed.

This function is most typically used prior to blastClassify16S to set up the database before searching and classifying. It can be seen as the 'training step' of a BLAST-based classification procedure.

The sequence must be a vector of DNA-sequences (16S sequences). The taxon is a vector of the same length as sequence, containing the correpsonding taxon information.

Value

The database files are created, and the name of the database (name) is returned.

Author(s)

Lars Snipen.

See Also

blastClassify16S.

Examples

# See examples for blastClassify16S.

microclass documentation built on Aug. 28, 2020, 5:08 p.m.