The applications listed here are available for use in the Discovery Environment and are documented in: Discovery Environment Manual.

Discovery Environment Applications List

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  1. Protein sequence file (makedb only)

    Note

    Please ignore this field and use DIAMOND-makedb-0.9.10 app instead for building the database for DIAMOND

  2. Input query sequence file: Name of the protein fasta file (query)
  3. DIAMOND database file: Path to the database that was created using DIAMOND-makedb-0.9.10

Parameters

  1. Maximum number of target sequences to report alignments for (default: 0)
  2. Minimum bit score to report alignments (overrides e-value setting) (default: 0)
  3. Minimum subject cover% to report an alignment (default: 0)
  4. Output file format: BLAST tabular, BLAST XML, BLAST tabular, DIAMOND alignment archive (DAA), SAM (default BLAST tabular)
  5. Report alignments within this percentage range of top alignment score (default: 0)
  6. Minimum identity% to report an alignment (default: 0)
  7.  Enable sensitive mode (default: fast)
  8. DIAMOND program (Required): Build DIAMOND database from a FASTA file, Align amino acid query sequences against a protein reference database, Align DNA query sequences against a protein reference database

    Note

    Please use either of "Align amino acid query sequences against a protein reference database" or "Align DNA query sequences against a protein reference database" depending on your query type. Do not select Build DIAMOND database from a FASTA file

  9. Output file format: Both strands, Minus strand, Plus strand (default: Both strands)
  10. Maximum e-value to report alignments (default: 0.001)
  11. Minimum query cover% to report an alignment (default: 0)
  12.  Enable more sensitive mode (default: fast)
  13. Output filename (default is output)

     

Test/sample data:


The test data are provided for testing DIAMOND -makedb- 0.9.10 is in here - /iplant/home/shared/iplantcollaborative/example_data/diamond_blast:

Use the following inputs/outputs for testing DIAMOND-makedb-0.9.10

  1. Mandatory argument

    1. Input file - sample.faa

    2. Database file - out (Default)

Output Reports:

  1. out.dmnd - Final database for the input file (sample.faa). Now you can proceed to actual DIAMOND Blast

 

  1. Inputs:

    1. Input query sequence file: msu-irgsp-proteins.fasta

    2. DIAMOND database file: out.dmnd

  2. Parameters:
    1. DIAMOND program (Required): Align amino acid query sequences against a protein reference database

Leave the rest of the parameters as default

Output Reports:

  1. output - Tablular BLASTP result
  2. Inputs that you submitted (msu-irgsp-proteins.fasta and out.dmnd)
  3. Logs (*.err and *.out)

More information about DIAMOND-makedb-0.9.10 can be found at https://github.com/bbuchfink/diamond

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