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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Create BLAST database

This application creates BLAST database from input sequence files, earlier this utility was called formatdb

App Creator

Nirav Merchant

Quick Start

  • If you need multiple input files to build a database use the "Concatenate Multiple File" utility in Apps 

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)

Single fasta file (for now, multiple files will be allowed in later version of this app). Use shrtjmptest.fa in the directory above as test input.

Parameters Used in App

  •  Input file and file type are required. 
  • Use default settings with test data.

Output File(s)

Blast formatted database. When run with the test data there will be an output directory called blastdatabase. This directory will contain three files all named with the prefix "blastdb" (blastdb.nhr, blastdb.nin, blastdb.nsq).

 

An example of how to use the "Create BLAST Database" app:

The Blastp and Blastn 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.

Tool Source for App

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