Local BLAST Search Element

Finds annotations for a DNA sequence in a local BLAST database.

Element type: blast-plus

BLAST+ is used as an external tool from UGENE and must be installed on your system. To learn more about the external tools, please read the main UGENE User Manual.

Parameters

Parameter	Description	Default value	Parameter in Workflow File	Type
Search type	Selects the type of the BLAST searches.	blastn	blast-type	string
	Available values are:
	* blastn
	* blastp
	* blastx
	* tblastn
	* tblastx
Database path	Path to the database files.		db-path	string
Database name	Base name for BLAST DB files.		db-name	string
Tool path	Path to the BLAST executable.	default	tool-path	string
Temporary directory	Directory for temporary files.	default	temp-dir	string
Expected value	Expectation threshold value.	10	e-val	numeric
Culling limit	If the query range of a hit is enveloped by at least this many higher-scoring hits, delete the hit.	0	max-hits	numeric
Annotate as	Name of the result annotations.	blast_result	result-name	string
Gapped alignment	Perform gapped alignment.	use	gapped-aln	boolean
Gap costs	Cost to create and extend a gap in an alignment.	2 2	gap-costs	string
Match scores	Reward and penalty for matching and mismatching bases.	1 -3	match-scores	string
BLAST output	Location of BLAST output file.		blast-output	string
BLAST output type	Type of BLAST output file.	XML (-outfmt 5)	type-output	string

Input/Output Ports

The element has 1 input port:

Name in GUI: Input sequence

Name in Workflow File: in-sequence

Slots:

Slot In GUI	Slot in Workflow File	Type
Sequence	sequence	sequence

And 1 output port:

Name in GUI: Annotations

Name in Workflow File: out-annotations

Slots:

Slot In GUI	Slot in Workflow File	Type
Set of annotations	annotations	annotation-table