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EMBOSS Sixpack

Introduction

Sixpack reads a DNA sequence and outputs the three forward and (optionally) three reverse translations in a visual manner.

Official Website
Download Software

How to use this tool

Running a tool from the web form is a simple multiple steps process, starting at the top of the page and following the steps to the bottom.

Each tool has at least 2 steps, but most of them have more:

  • The first steps are usually where the user sets the tool input (e.g. sequences, databases...)
  • In the following steps, the user has the possibility to change the default tool parameters
  • And finally, the last step is always the tool submission step, where the user can specify a title to be associated with the results and an email address for email notification. Using the submit button will effectively submit the information specified previously in the form to launch the tool on the server

Note that the parameters are validated prior to launching the tool on the server and in the event of a missing or wrong combination of parameters, the user will be notified directly in the form.

Step 1 - Input Sequences

Input Sequence

A DNA sequence can be entered or pasted into this box. Ideally use a known sequence format such as fasta or EMBL, text pasted from word processors may contain meta-characters that cause problems.

Sequence File Upload

Upload a file containing DNA sequence ideally in a known sequence format such as fasta or EMBL, Word processor files may contain meta-characters that cause problems.

Step 2 - Select Parameters

Codon Table

Which Genetic Code table to use. These are kept synchronised with those maintained at the NCBI's Taxonomy Browser.

Table name Value
Standard Code 0
Vertebrate Mitochondrial 2
Yeast Mitochondrial 3
Mold, Protozoan, Coelenterate Mitochondrial and Mycoplasma/Spiroplasma 4
Invertebrate Mitochondrial 5
Ciliate Macronuclear and Dasycladacean 6
Echinoderm Mitochondrial 9
Euplotid Nuclear 10
Bacterial 11
Alternative Yeast Nuclear 12
Ascidian Mitochondrial 13
Flatworm Mitochondrial 14
Blepharisma Macronuclear 15
Chlorophycean Mitochondrial 16
Trematode Mitochondrial 21
Scenedesmus obliquus 22
Thraustochytrium Mitochondrial 23

Default value is: Standard Code [0]

First ORF

Count the beginning of a sequence as a possible ORF, even if it's inferior to the minimal ORF size.

Default value is: yes [true]

Last ORF

Count the end of a sequence as a possible ORF, even if it's not finishing with a STOP, or inferior to the minimal ORF size.

Default value is: yes [true]

Reverse

Choose this option if you wish to reverse and compliment your sequence.

Default value is: yes [true]

ORF Min Size

Minimum size of Open Reading Frames (ORFs) to display in the translations.

Default value is: 1

Step 3 - Submission

Job title

It's possible to identify the tool result by giving it a name. This name will be associated to the results and might appear in some of the graphical representations of the results.

Email Notification

Running a tool is usually an interactive process, the results are delivered directly to the browser when they become available. Depending on the tool and its input parameters, this may take quite a long time. It's possible to be notified by email when the job is finished by simply ticking the box "Be notified by email". An email with a link to the results will be sent to the email address specified in the corresponding text box. Email notifications require valid email addresses.

Email Address

If email notification is requested, then a valid Internet email address in the form joe@example.org must be provided. This is not required when running the tool interactively (The results will be delivered to the browser window when they are ready).

References

EMBOSS: the European Molecular Biology Open Software Suite.
(2000 June 01) Trends in genetics : TIG 16 (6) :276-277
The EMBL-EBI bioinformatics web and programmatic tools framework.
(2015 April 06) Nucleic acids research 43 (W1) :W580-4
Analysis Tool Web Services from the EMBL-EBI.
(2013 May 13) Nucleic acids research 41 (Web Server issue) :W597-600