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

Parameters in GUI

Parameter	Description	Default value
Database (required)	Selects the database to search through. Available databases are blastn, blastp and cdd.	ncbi-blastn
Annotate as	Name of the result annotations.
Expected value	This parameter specifies the statistical significance threshold of reporting matches against the database sequences.	10
Max hits	Maximum number of hits. The maximum available number is 5000.	10
Short sequence	Optimizes search for short sequences.	False
Entrez query	Enter an Entrez query to limit search.
Annotate as	Name of the result annotations.
BLAST output	Location of the BLAST output file. This parameter insignificant for cdd search.


Gap costs	Cost to create and extend a gap in an alignment.	2 2
Match scores	Reward and penalty for matching and mismatching bases.	1 -3

Parameters in

Schema File

Workflow File

Type: blast-ncbi

Parameter	Parameter in the GUI	Type
db	Database	string Available values are: ncbi-blastn ncbi-blastp ncbi-cdd
result-name	Annotate as	string
e-val	Expected value	string
max-hits	Max hits	numeric
short-sequence	Short sequence	boolean
entrez-query	Entrez query	string
result-name	Annotate as	string
blast-output	BLAST output	string

gap-costs	Gap costs	string
match-scores	Match scores	string

Input/Output Ports

The element has 1 input port:

Name in GUI: Input sequence

Name in Schema File Workflow File: in-sequence

Slots:

Slot In GUI	Slot in Schema Workflow File	Type
Sequence	sequence	sequence

And 1 output port:

Name in GUI: Annotations

Name in Schema File Workflow File: out-annotations

Slots:

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