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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KOBAS

KEGG Orthology Based Annotation System (KOBAS) is a standalone Python application in Bioinformatics. KOBAS can assign appropriate KO terms for queried sequences based on similarity search, and it can further discover
enriched KO terms among the annotation results by frequency of pathways or statistical significance of pathways.

Quick Start

Test Data

(info)

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

Input File(s)

Use CFLO_1.fa from the directory above as test input.

Parameters Used in App

Use the these parameters with test data:

select protein FASTA as the input file type

use 'dme' as the species code (Species codes can be looked up here: https://www.kegg.jp/kegg/catalog/org_list.html)

Output File(s)

seq_pep folder --contains the BLAST database files that were used

  • dme.pep.fasta (and corresponding .phr, pin, pog, psd, psi, psq files)

sqlite3–contains the database files used to annotate your data

  • dme.db
  • organism.db

dme.tsv–tabular BLAST output

kobas_annotate_out.txt–KOBAS annotate output (this can be used as input for KOBAS identify)

Tool Source for App

https://github.com/AgBase/kobas

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