Introduction
Sixpack reads a DNA sequence and outputs the three forward and (optionally) three reverse translations in a visual manner.
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Important Note
- We kindly ask all users of EMBL-EBI Web Services to submit tool jobs in batches of no more than 30 at a time and not to submit more until the results and processing is complete. Please ensure that a valid email address is provided. Excessive usage of a particular resource will be dealt with in accordance with EMBL-EBI's Terms of Use. Please contact us if you need further information.
How to Access EMBOSS sixpack
EMBOSS sixpack can be accessed via
Web Form
Web interface for EMBOSS sixpack is available at : https://www.ebi.ac.uk/Tools/st/emboss_sixpack/
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. (See example input formats). 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. (See example input formats). 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 |
| Candidate Division SR1, Gracilibacteria | 25 |
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).
Web Services
Web Services are available using REST and SOAP protocols that enable programmatic access and allow their integration into other applications and analytical workflows and pipelines.
For an introduction on how to run these clients and use them in workflows please see the webinar series.
REST API
The Representational State Transfer (REST) sample clients are provided for a number of programming languages. For details of how to use these clients, download the client and run the program without any arguments.
| Language | Download | Requirements |
|---|---|---|
| Perl | emboss_sixpack.pl | LWP and XML::Simple |
Python | xmltramp2 |
For details see Environment setup for REST Web Services and Examples for Perl REST Web Services Clients pages.
WADL
The WADL for the EMBOSS sixpack (REST) service: http://www.ebi.ac.uk/Tools/services/rest/emboss_sixpack?wadl
Tool parameters
Parameters | Command line parameter |
|---|---|
| --codontable |
SOAP API
The Simple Object Access Protocol (SOAP) sample clients are provided for a number of programming languages. For details of how to use these clients, download the client and run the program without any arguments.
WSDL
The WSDL for the EMBOSS sixpack (SOAP) service: http://www.ebi.ac.uk/Tools/services/soap/emboss_sixpack?wsdl
Open API Interface
https://www.ebi.ac.uk/Tools/common/tools/help/index.html?tool=emboss_sixpack
Common Workflow Language
CWL (Common Workflow Language) implementation for consuming EMBL-EBI Bioinformatics Web Services tools' clients are available at https://github.com/ebi-wp/webservice-cwl
For details, see CWL Workflows page.