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Rationale and Background

Blastn-2.6.0+ compares a nucleotide query sequence against a nucleotide sequence database. The program aligns sequence (input file) on the base prepared by program makeblastdb.

Mandatory arguments

  • Inputs: Path to the query file name. Nucleotide sequences in fasta format
  • Database: Path to the Database folder prepared by makeblastdb
  • Output File Name: Name of the output file


  • e-value: Expect value (E) for saving hits (Default is 10.0)
  • Output Format: Format of the output file (Default is "flat query anchored with identities")
  • gapped vs ungapped alignment: Whether to perform gapped or ungapped alignment
  • Option1 and Option2 are your favorite additional blastn parameters that you want to specify. For example, if you want to keep only one best bit out of several many hits for the same query id then you put -num_alignments 1 in the Option1 box. For more details about Blastn parameters please visit Blast documentation page here

Test Run

All files are located in the Community Data directory of the CyVerse Discovery Environment at the following path:

Community Data > iplantcollaborative > example_data > blastn (/iplant/home/shared/iplantcollaborative/example_data/blastn)

Mandatory arguments: 

  • Inputs: shrtjmptest.fa
  • Database: blastdatabase
  • Output File Name: final_out.txt


  • e-value: 10.0 (Default)
  • Output Format: "flat query anchored with identities" (Default)
  • gapped vs ungapped alignment: gapped
  • Option1num_alignments 1


  • final_out.txt