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 seqret

seqret reads in one or more sequences and writes them out again. The sequence input may be a literal sequence or read from a database, file, file of sequence names, or even the command-line or the output of another programs. The sequence output can be written to screen, to file, or passed to another program.

Quick Start

To use seqret,

  1. upload your input data in most format, such as fasta, GenBank, Embl, or Emsembl, gcg formats.
  2. Choose your option, such as reverse
  3. Select your output sequence format
  4. 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 -> X65923.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.

  • Default parameters only, no further configuration needed.

Output File(s)

Standard EMBOSS output sequence file.

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

Tool Source

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