Page History

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
Database	Select the database to search through.		db

 

string
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 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

Parameters in Workflow File

Type: blast-ncbi

ParameterParameter in the GUITypedbDatabase

string

Available values are:

ncbi-blastndbDatabasestringe-valExpected valuestringhitsResults limitnumericmegablastMegablastbooleanshort-sequenceShort sequencebooleanentrez-queryEntrez querystringresult-nameAnnotate asstringblast-outputBLAST outputstringgap-costsGap costsstring

ncbi-blastp

ncbi-cdd

match-

scoresMatch

scores

string

The element has 1 input port:

Name in GUI: Input sequence

Name in Workflow File: in-sequence

Slots:

And 1 output port:

Name in GUI: Annotations

Name in Workflow File: out-annotations

Slots: