Remote BLAST Element

Finds annotations for the supplied DNA sequence in the NCBI remote database.

Element type: blast

Parameters

Parameter	Description	Default value	Parameter in Workflow File	Type
Database	Selects the database to search through. Available databases are blastn, blastp, and cdd.	ncbi-blastn	db	string
	Available values are:
	* ncbi-blastn
	* ncbi-blastp
	* ncbi-cdd
Expected value	This parameter specifies the statistical significance threshold of reporting matches against the database sequences.	10	e-val	string
Results limit	The maximum number of results.	10	hits	numeric
Megablast	Use megablast.	False	megablast	boolean
Short sequence	Optimizes search for short sequences.	False	short-sequence	boolean
Entrez query	Enter an Entrez query to limit search.		entrez-query	string
Annotate as	Name of the result annotations.		result-name	string
BLAST output	Location of the BLAST output file. This parameter is insignificant for cdd search.		blast-output	string
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

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