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

Element type: blast

Parameters

ParameterDescriptionDefault valueParameter in Workflow FileType
Database Selects the database to search through. Available databases are blastn, blastp and cdd.ncbi-blastndb

string

Available values are:

  • ncbi-blastn
  • ncbi-blastp
  • ncbi-cdd
DatabaseSelect the database to search through.
dbstring
Expected valueThis parameter specifies the statistical significance threshold of reporting matches against the database sequences.10e-valstring
Results limitThe maximum number of results.10hitsnumeric
MegablastUse megablast.Falsemegablastboolean
Short sequenceOptimizes search for short sequences.Falseshort-sequenceboolean
Entrez queryEnter an Entrez query to limit search.
entrez-querystring
Annotate asName of the result annotations.
result-namestring
BLAST outputLocation of the BLAST output file. This parameter insignificant for cdd search.
blast-outputstring
Gap costsCost to create and extend a gap in an alignment.2 2gap-costsstring
Match scoresReward and penalty for matching and mismatching bases.1 -3match-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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