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Blast

Basic local alignment search tool.

Version 1.0
Bundle sequencing
Categories Alignment
Authors Ping Chen (ping.chen@helsinki.fi)
Issue tracker View/Report issues
Requires installer (bash)
Source files component.xml blastcomp.sh
Usage Example with default values

Inputs

Name Type Mandatory Description
query FASTA Mandatory Short sequences in fasta format.
dbSeq FASTA Mandatory Search set for sequence database.

Outputs

Name Type Description
result CSV Detailed information for the aligned records.

Parameters

Name Type Default Description
dbName string "db" The name of sequence database.
evalue float 10 Expectation value. The default is 10.
nProcessor int 1 Number of processors to use.
program string "blastn" Blast program name. It can be one of 'blastn', 'blastp', 'blastx', 'tblastn' and 'tblastx'. 'blastn' is for searching a nucleotide database using a nucleotide query; 'blastp' is for searching protein database using a protein query; 'blastx' is for searching protein database using a translated nucleotide query; 'tblastn' is for searching translated nucleotide database using a protein query; 'tblastx' is for searching translated nucleotide database using a translated nucleotide query.
sequenceType string "F" The type of database sequences. 'F' (nucleotide) or 'T' (protein).
wordSize int 0 Word size, default if zero (blastn 11, megablast 28, all others 3).

Test cases

Test case Parameters IN
query
IN
dbSeq
OUT
result
case1 properties query dbSeq result

wordSize=21,
program=blastn


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