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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Rationale:


Blastdbcmd-batch-2.6.0 is used for extracting sequence data from a blast database. It dumps a select set of sequences from a BLAST database

Blastdbcmd-batch-2.6.0 is invoked using the following:

  1. Input (s)
    1. Blast Database 
    2. Molecule type
    3. Sequence Identifier (batch/multiple)
  2. Output
    1. Default file name - BlastOutput

Please work through the documentation and add your comments on the bottom of this page, or email comments to support@cyverse.org. Thank you.

Test Data

 The test data 

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All files are located in the Community Data directory of the iPlant Discovery Environment at the following path: Community Data > iplantcollaborative > example_data > makeblastdb (/iplant/home/shared/iplantcollaborative/example_data/makeblastdb/)

Run Create_BLAST_database-2.6.0__with_parse_seqids_option as following:

  1. Input (s)
    1. Blast Database : /iplant/home/shared/iplantcollaborative/example_data/makeblastdb
    2. Molecule type: protein
    3. Sequence Identifier (batch): /iplant/home/shared/iplantcollaborative/example_data/batch_list.txt
  2. Output
    1. Default file name - BlastOutput containing the following output

 

Tool Source for App