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 support@cyverse.org.

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

Rationale and Background

Blastn-2.6.0+ compares an 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

Parameters

  • 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

Parameters:

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

Output

  • final_out.txt