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  • Local BLAST Search Element

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Database path (required)blastndefault
ParameterDescriptionDefault value
Database name (required)Base name for BLAST DB files. 
Search typeSelects the type of the BLAST searches.blastn
Database pathPath to the database files. 
Database nameBase name for BLAST DB files. 
Tool path (required)Path to the BLAST executable.defaultSearch type (required)Selects the type of the BLAST searches.
Temporary directoryDirectory for temporary files.default
Expected valueExpectation threshold value.10
Annotate asName of the result annotations.misc_feature
Expected valueExpectation threshold value.10
Temporary directory (required)Directory for temporary files.blast_result
Gapped alignmentPerform gapped alignment.use
Gap costsCost to create and extend a gap in an alignment.2 2
Match scoresReward and penalty for matching and mismatching bases.1 -3
BLAST outputLocation of BLAST output file. 
BLAST output typeType of BLAST output file.XML (-m 7)

Parameters in Workflow File

Type: blast

name name
ParameterParameter in the GUIType
blast-typeSearch type

string

Available values are:

  • blastn
  • blastp
  • blastx
  • tblastn
  • tblastx
db-pathDatabase pathstring
db-pathnameDatabase pathnamestring
tool-pathTool pathstring
blasttemp-typedirSearch typeTemporary directory

string

Available values are:

  • blastn
  • blastp
  • blastx
  • tblastn
  • tblastx
e-valExpected valuenumeric
result-nameAnnotate asstring
e-valExpected valuenumeric
temp-dirTemporary directory
gapped-alnGapped alignmentboolean
gap-costsGap costsstring
match-scoresMatch scoresstring
blast-outputBLAST outputstring
type-outputBLAST output typestring

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