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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The CyVerse App Store is currently being restructured, and apps are being moved to an HPC environment. During this transition, users may occasionally be unable to locate or use apps that are listed in our tutorials. In many cases, these apps can be located by searching them using the search bar at the top of the Apps window in the DE. To increase the chance for search success, try not searching the entire app name and version number but only the portion that refers to the app's function or origin (e.g. 'SOAPdenovo' instead of 'SOAPdenovo-Trans 1.01').

Also, as part of the 2.8 app categorization, a number of apps were deprecated and are no longer available, and there is no longer an Archive category. You can search for a suitable replacement in the List of Applications in this window, or search on an app name or tool used for an app in the Apps window search field. If you need an app reinstated, please contact

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

Rationale and Background

The makeblastdb application produces BLAST databases from FASTA files. In the simplest case the FASTA definition lines are not parsed by makeblastdb and may be completely unstructured. The text in the definition line will be stored in the BLAST database and displayed in the BLAST report


  • Leave these as default


  • With plant.118.1.genomic.fna as input file and nucleotide as sequence format
    • blastdb_n.nhr
    • blastdb_n.nin
    • blastdb_n.nsq
  • With plant.118.protein.faa as input file and protein as sequence format
    • blastdb_p.phr
    • blastdb_p.pseq


The Blastp-2.6.0+ and  Blastn-2.6.0+ apps take a folder as input for the database because there are multiple files involved. The best thing to do when you are creating a database is to give the database and the output file the same name e.g. "mygenome". Then after it has run, make a new folder inside the output directory, name it "mygenome", and drag all the database files into it, but not the logs directory. You can then drag that directory "mygenome" to one of your other directories so it will be easy to find. When you run Blastp or Blastn drag and drop the database directory you created into the database input for Blastp/Blastn

Please work through the documentation and add your comments on the bottom of this page, or email comments to or click the intercom button on this page. Thank you.


For more options of makeblastdb visit this page