NCBI BLAST+ integrated into Galaxy

GigaScience

Table 1 NCBI BLAST+ Galaxy tools

Galaxy tool name	Description	Reference(s)
NCBI BLAST+ blastp	Protein vs protein	[1, 16]
NCBI BLAST+ blastn	Nucleotide vs nucleotide	[1, 16]
NCBI BLAST+ blastx	Translated nucleotide vs protein	[1, 16]
NCBI BLAST+ tblastn	Protein vs translated nucleotide	[1, 16]
NCBI BLAST+ tblastx	Translated nucleotide vs translated nucleotide	[1, 16]
NCBI BLAST+ makeblastdb	Make BLAST nucleotide or protein database	[1, 16]
NCBI BLAST+ makeprofiledb	Make BLAST protein domain database	[1, 16]
NCBI BLAST+ blastdbcmd entry(s)	Extract sequence(s) from BLAST database	[1, 16]
NCBI BLAST+ blastdbcmd info	Show BLAST database information	[1, 16]
NCBI BLAST+ dustmasker	Nucleotide masking using the DUST algorithm	[1, 16]
NCBI BLAST+ segmasker	Protein masking using the SEG algorithm	[1, 16]
NCBI BLAST+ windowmasker	Window-based sequence masker	[1, 16]
NCBI BLAST+ convert2blastmask	Lowercase masking	[1, 16]
NCBI BLAST+ rpsblast	Protein vs protein domain	[16, 39]
NCBI BLAST+ rpstblastn	Translated nucleotide vs protein domain	[16, 39]

Each row lists a separate Galaxy tool, all available from https://toolshed.g2.bx.psu.edu/view/devteam/ncbi_blast_plus/ on the Galaxy Tool Shed [9]. A separate Galaxy tool is listed for each different underlying NCBI BLAST+ command line tool, except for the blastdbcmd command line tool, whose two main functions are represented as two separate Galaxy tools. We intend to add further wrappers later, including for the command line tools psiblast and deltablast

ISSN: 2047-217X