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

Parameters in GUI

ParameterDescriptionDefault value
Database Selects the database to search through. Available databases are blastn, blastp and cdd.ncbi-blastn
DatabaseSelect the database to search through. 
Expected valueThis parameter specifies the statistical significance threshold of reporting matches against the database sequences.10
Results limitThe maximum number of results.10
MegablastUse megablast.False
Short sequenceOptimizes search for short sequences.False
Entrez queryEnter an Entrez query to limit search. 
Annotate asName of the result annotations. 
BLAST outputLocation of the BLAST output file. This parameter insignificant for cdd search. 
Gap costsCost to create and extend a gap in an alignment.2 2
Match scoresReward and penalty for matching and mismatching bases.1 -3

Parameters in Workflow File

Type: blast-ncbi

ParameterParameter in the GUIType
dbDatabase

string

Available values are:

  • ncbi-blastn
  • ncbi-blastp
  • ncbi-cdd
dbDatabasestring
e-valExpected valuestring
hitsResults limitnumeric
megablastMegablastboolean
short-sequenceShort sequenceboolean
entrez-queryEntrez querystring
result-nameAnnotate asstring
blast-outputBLAST outputstring
gap-costsGap costsstring
match-scoresMatch scoresstring

Input/Output Ports

The element has 1 input port:

Name in GUI: Input sequence

Name in Workflow File: in-sequence

Slots:

Slot In GUISlot in Workflow FileType
Sequencesequencesequence

And 1 output port:

Name in GUI: Annotations

Name in Workflow File: out-annotations

Slots:

Slot In GUISlot in Workflow FileType
Set of annotationsannotationsannotation-table
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