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 master copies of EMBOSS documentation are available at http://emboss.open-bio.org/wiki/Appdocs on the EMBOSS Wiki.

EMBOSS transeq

Description

transeq reads one or more nucleotide sequences and writes the corresponding protein sequence translations to file. It can translate in any of the 3 forward or three reverse sense frames, or in all three forward or reverse frames, or in all six frames. The translation may be restricted to specified regions, for example, corresponding to the coding regions of your sequences. It can translate using the standard ('Universal') genetic code and also with a selection of non-standard codes.

Quick Start

To use sixpack,

  1. upload your input nucleotide sequence in most format, such as fasta, GenBank, Embl, or Emsembl, gcg formats.
  2. Choose your option, such as genetic code table
  3. launch your job

Test Data

 

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Test data for this app can be found here:  Community Data -> iplantcollaborative -> example_data ->EMBOSS

Input File

The input can be in most sequence format, such as fasta, gcg, GenBank, Embl, and Ensembl formats. 

Test input in GenBank sequence format: Community Data -> iplantcollaborative -> example_data ->EMBOSS -> Input -> test_trans.fa

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)

Standard EMBOSS output sequence file.

  • Expected output files: transeq_out.fa

Tool Source

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