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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TransDecoder 5.5.0

Finds open reading frames in transcripts and predicts coding regions. TransDecoder has two functions. This app runs both functions as a pipeline.

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 -> TransDecoder

Input File(s)

Use example_nt.fa from the directory above as test input in BOTH the extract long ORFs and  predict coding regions sections

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.

  • Use these parameters within the DE app interface:
    • in the 'predict coding regions' 'options' section: choose 'dynamic' in the 'retain long ORFs mode field

Output File(s)

Expect these output files. For the test case, the output files you will find in the example_data directory are:

example_nt.fa.transdecoder_dir--output directory from the 'extract long ORFs' process

  • base_freqs.dat
  • longest_orfs.cds
  • longest_orfs.gff3
  • longest_orfs.pep

detect_coding_regions_output-- output directory from the 'predict coding regions' process

  • example_nt.fa.transdecoder.bed
  • example_nt.fa.transdecoder.cds
  • example_nt.fa.transdecoder.gff3
  • example_nt.fa.transdecoder.pep

In both cases the .pep file is a peptide FASTA file.

Tool Source for App

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