EMBOSS Transeq

Introduction

A program to translate nucleic acid sequences to their corresponding peptide sequences. It can translate to the three forward and three reverse frames, and output multiple frame translations at once.

FAQs
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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

One or more nucleic acide sequences to be translated can be entered directly into this form. Any input formats accepted by EMBOSS can be used, the full list of sequence formats accepted as input by EMBOSS tools is given in this table: <a href="http://emboss.open-bio.org/html/use/ch05s02.html#d0e5958" target ="_blank">EMBOSS sequence formats</a>. Adding a return to the end of the sequence may help certain applications understand the input. Note that directly using data from word processors may yield unpredictable results as hidden/control characters may be present.

Sequence File Upload

A file containing one or more valid sequences in any EMBOSS accepted format can be uploaded and used as input for the translation. The full list of sequence formats accepted as input by EMBOSS tools is given in this table: <a href="http://emboss.open-bio.org/html/use/ch05s02.html#d0e5958" target ="_blank">EMBOSS sequence formats</a>. Word processor files may yield unpredictable results as hidden/control characters may be present in the files. It is best to save files with the Unix format option to avoid hidden Windows characters.

Step 2 - Select parameters

Frame

The frames to be translated. The order of the frames follows the Staden convention: Frame -1 is the reverse-complement of the sequence having the same codon phase as frame 1. Frame -2 is the same phase as frame 2. Frame -3 is the same phase as frame 3.

Frame Value
1 1
2 2
3 3
F (Forward three frames) F
-1 -1
-2 -2
-3 -3
R (Reverse three frames) R
6 (All six frames) 6

Default value is: 1

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]

Regions

Which regions of the user's DNA molecule are to be translated.

Default value is: START-END

Trim

Remove "*" and "X" (stop and ambiguity) symbols from the end of the translation.

Default value is: no [false]

Reverse

Choose this option if you wish to reverse and complement your input sequence before frame translation.

Default value is: no [false]

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 Jun) Trends in genetics : TIG 16 (6) :276-7
A new bioinformatics analysis tools framework at EMBL-EBI.
(2010 Jul) Nucleic acids research 38 (Web Server issue) :W695-9
Analysis Tool Web Services from the EMBL-EBI.
(2013 Jul) Nucleic acids research 41 (Web Server issue) :W597-600