Description Usage Arguments Details Value Author(s) See Also Examples
Building a BLAST database for 16S based classification.
1 | blastDbase16S(name, sequence, taxon)
|
name |
The name of the database (text). |
sequence |
A character vector with 16S sequence data. |
taxon |
A character vector with taxon information. |
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.
The database files are created, and the name of the database (name
) is returned.
Lars Snipen.
1 | # See examples for blastClassify16S.
|
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