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Finds annotations for the supplied DNA sequence in local BLAST database.

 

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BLAST is used as an external tool from UGENE and it must be installed on your system. To learn more about the external tools, please, read main UGENE User Manual.

Parameters in GUI

 

ParameterDescriptionDefault value
Search typeSelects the type of the BLAST searches.blastn
Database pathPath to the database files. 
Database nameBase name for BLAST DB files. 
Tool path Path to the BLAST executable.default
Temporary directoryDirectory for temporary files.default
Expected valueExpectation threshold value.10
Best hits limitSpecifies the number of best hits from a region of the query to keep. 0 turns it off. If used, 100 is recommended.0
Annotate asName of the result annotations.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

ParameterParameter in the GUIType
blast-typeSearch type

string

Available values are:

  • blastn
  • blastp
  • blastx
  • tblastn
  • tblastx
db-pathDatabase pathstring
db-nameDatabase namestring
tool-pathTool pathstring
temp-dirTemporary directory

string

e-valExpected valuenumeric
max-hitsBest hits limitnumeric
result-nameAnnotate asstring
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
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