Child pages
  • Local BLAST Search Element

Versions Compared

Key

  • This line was added.
  • This line was removed.
  • Formatting was changed.
Comment: Migrated to Confluence 5.3

...

 

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
Max 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-hitsMax Best hits limitnumeric
result-nameAnnotate asstring
gapped-alnGapped alignmentboolean
gap-costsGap costsstring
match-scoresMatch scoresstring
blast-outputBLAST outputstring
type-outputBLAST output typestring

Input/Output Ports

...