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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Blastn-2.2.26 

Nucleotide sequence mapping against a small, focused database of DNA sequences.

App Creator

Roger Barthelson

Quick Start

Test Data

Icon

Test data for this app appears directly in the Discovery Environment in the Data window under Community Data -> iplantcollaborative -> example_data -> blastn.

Input File(s)

Use shrtjmptest.fa and the blastdatabase folder from the directory above as test input.

Parameters Used in App

When the app is run in the Discovery Environment, use the following parameters with the above input file(s) to get the output provided in the next section below.

  • Default parameters only, no further configuration needed.

 

Output File(s)

Expect a text file named as set in the input section as output. For the test case, the output file you will find in the example_data directory is named BlastOutput.

General use with the "Create BLAST Database" app:

The Blastn app takes 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 Blastn, drag and drop the database directory you created into the database input for Blastn. 

Tool Source for App

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