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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 sixpack

sixpack reads a DNA sequence and writes an output file giving out the forward and reverse sense sequences with the three forward and (optionally) three reverse translations in a pretty display format. A genetic code may be specified for the translation. There are various options to control the appearance of the output file. It also writes a file of protein sequences corresponding to any open reading frames that are larger than the specified minimum size: the default of 1 base shows all possible open reading frames.

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

• Resource: More information on input sequence feature and format could be found at https://pods.iplantcollaborative.org/wiki/display/sciplant/EMBOSS+Sequence+Feature+Format

Test Data

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/sixpack.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.

• 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  -> sixpack.report and sixpack.seq

Tool Source

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