makeBlastDb: Make Blast Database

In packFinder: de novo Annotation of Pack-TYPE Transposable Elements

Description

Generates a BLAST database to be queried. Required for identifying sequences using the BLAST+ software.

Usage

makeBlastDb(fastaFile, dbPath, blastPath, dbType = "nucl")

Arguments

fastaFile	FASTA file containing sequences to generate a BLAST database from.
dbPath	Path to save the BLAST database to.
blastPath	Path/name of BLAST program to use. Name of the application for Linux/MacOS, absolute path for the executable for windows users.
dbType	Type of BLAST database to create, e.g. "nucl" for a nucleotide database.

Value

No return value; generates a blast database in the chosen directory.

Author(s)

Jack Gisby

References

For further information, see the NCBI BLAST+ application documentation and help pages (https://www.ncbi.nlm.nih.gov/pubmed/20003500?dopt=Citation).

See Also

packSearch

Examples

## Not run: 
makeBlastDb("genes.fasta", "blastdb.db", "C:/blast.exe")

## End(Not run)

packFinder documentation built on Nov. 8, 2020, 5:24 p.m.