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 cusp

cusp calculates a codon usage table for one or more nucleotide coding sequences and writes the table to file.

Quick Start

To use cusp,

  1. upload your input sequence data in most format, such as fasta, GenBank, Embl, or Emsembl, gcg formats.
  2. choose your option, type in start and end sequence position
  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. For details, please see http://emboss.sourceforge.net/apps/release/6.0/emboss/apps/seqret.html

  • Test input in GenBank sequence format: Community Data -> iplantcollaborative -> example_data ->EMBOSS ->Input -> X13776.txt

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.

  • In Application options, type in Start and End sequence positions.

Output File(s)

Standard EMBOSS output sequence file.

  • Expected output files: Community Data -> iplantcollaborative -> example_data -> EMBOSS -> Output -> cusp.output

Tool Source

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