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 DE Quick Start tutorial provides an introduction to basic DE functionality and navigation.

Please work through the tutorial and add your comments to the bottom of this page. Or send comments per email to support@cyverse.org. Thank you.

Rationale and background: 

DIAMOND is a sequence aligner for protein and translated DNA searches, designed for high-performance analysis of big sequence data. The key features are: 

  • Pairwise alignment of proteins and translated DNA at 500x-20,000x speed of BLAST.
  • Frameshift alignments for long read analysis.
  • Low resource requirements and suitable for running on standard desktops or laptops.
  • Various output formats, including BLAST pairwise, tabular and XML, as well as taxonomic classification.

 Pre-Requisites

  1. A CyVerse account. (Register for a CyVerse account here - user.cyverse.org)

Mandatory

  1. Input File: Name of the protein fasta file
  2. Database file name: Name of the outputted database file (Default is out)

Test/sample data:


The test data are provided for testing DIAMOND-makedb-0.9.10 is in here - /iplant/home/shared/iplantcollaborative/example_data/diamond_blast:

Use the following inputs/outputs for testing DIAMOND-makedb-0.9.10

  1. Mandatory argument

    1. Input file - sample.faa

    2. Database file - out (Default)

Output Reports:

  1. out.dmnd - Final database for the input file (sample.faa). 

    Now you can proceed to actual DIAMOND Blast

More information about DIAMOND-makedb-0.9.10 can be found at https://github.com/bbuchfink/diamond

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