EMBOSS Backtranseq

Introduction

A program to back-translate a protein sequence to a nucleotide sequence.

Official Website
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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 sequences to be translated can be entered directly into this form. Sequences can be be in GCG, FASTA, EMBL, GenBank, PIR, NBRF, PHYLIP or UniProtKB/Swiss-Prot format. Partially formatted sequences are not accepted. 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 format (GCG, FASTA, EMBL, GenBank, PIR, NBRF, PHYLIP or UniProtKB/Swiss-Prot) can be uploaded and used as input for the translation. 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

Codon Usage Table

Codon usage table name

Table name Value
Homo sapiens Ehuman.cut
Acinetobacter calcoaceticus Eacica.cut
Agrobacterium tumefaciens str C58 Eagrtu.cut
Anabaena sp Eanasp.cut
Arabidopsis thaliana Earath.cut
Azotobacter vinelandii Eazovi.cut
Bacillus megaterium Ebacme.cut
Geobacillus stearothermophilus Ebacst.cut
Bacillus subtilis Ebacsu.cut
Bacillus subtilis (high) Ebacsu_high.cut
Bombyx mori (silkmoth) Ebommo.cut
Bos taurus Ebovin.cut
Bacteriophage phi-X174 Ebpphx.cut
Bradyrhizobium japonicum USDA 110 Ebraja.cut
Brassica napus (rape) Ebrana.cut
Brachydanio rerio (zebrafish) Ebrare.cut
Caenorhabditis elegans (nematode) Ecaeel.cut
Candida albicans Ecanal.cut
Canis familiaris (dog) Ecanfa.cut
Caulobacter crescentus CB15 Ecaucr.cut
Gallus gallus (chicken) Echick.cut
Chlamydomonas reinhardtii Echlre.cut
Chlamydia trachomatis D UW-3 CX Echltr.cut
Clostridium acetobutylicum ATCC 824 Ecloab.cut
Cricetulus greseus (hamster) Ecrigr.cut
Cyanophora paradoxa Ecyapa.cut
Bradyrhizobium japonicum USDA 110 Ebraja.cut
Brassica napus (rape) Ebrana.cut
Brachydanio rerio (zebrafish) Ebrare.cut
Caenorhabditis elegans (nematode) Ecaeel.cut
Candida albicans Ecanal.cut
Canis familiaris (dog) Ecanfa.cut
Caulobacter crescentus CB15 Ecaucr.cut
Gallus gallus (chicken) Echick.cut
Chlamydomonas reinhardtii Echlre.cut
Chlamydia trachomatis D UW-3 CX Echltr.cut
Clostridium acetobutylicum ATCC 824 Ecloab.cut
Cricetulus greseus (hamster) Ecrigr.cut
Cyanophora paradoxa Ecyapa.cut
Dictyostelium discoideum Edicdi.cut
Dictyostelium discoideum (high) Edicdi_high.cut
Drosophila melanogaster Edrome.cut
Drosophila melanogaster (high) Edrome_high.cut
Escherichia coli K12 Eecoli.cut
Escherichia coli K12 (high) Eecoli_high.cut
Emericella nidulans Eemeni.cut
Emericella nidulans mitochondrion Eemeni_mit.cut
Emericella nidulans highly expressed Eemeni_high.cut
Erwinia carotovora subsp atroseptica SCRI1043 Eerwct.cut
Haemophilus influenzae Rd KW20 Ehaein.cut
Haloarcula marismortui ATCC 43049 (Halobacterium marismortui) Ehalma.cut
Halobacterium salinarum NRC-1 (Halobacterium halobium) Ehalsa.cut
Hordeum vulgare subsp vulgare (Barley) Ehorvu.cut
Klebsiella pneumoniae Eklepn.cut
Kluyveromyces lactis NRRL Y-1140 Eklula.cut
Lactococcus lactis subsp lactis Il1403 L. delbrueckii subsp lactis Elacdl.cut
Lycopersicon esculentum (tomato) Elyces.cut
Macaca fascicularis Emacfa.cut
Zea mays Emaize.cut
Zea mays chloroplast Emaize_chl.cut
Mammalian species (high) Emammal_high.cut
Manduca sexta Emanse.cut
Marchantia polymorpha chloroplast (liverwort) Emarpo_chl.cut
Medicago sativa Emedsa.cut
Methanothermobacter thermautotrophicus str Delta H Emetth.cut
Mus musculus Emouse.cut
Mycobacterium tuberculosis H37Rv Emyctu.cut
Neisseria gonorrhoeae Eneigo.cut
Neurospora crassa Eneucr.cut
Oncorhynchus mykiss (rainbow trout) Eoncmy.cut
Oryza sativa (rice) Eorysa.cut
Oryza sativa chloroplast (rice) Eorysa_chl.cut
Pisum sativum (pea) Epea.cut
Petunia x hybrida Epethy.cut
Phaseolus vulgaris Ephavu.cut
Sus scrofa (pig) Epig.cut
Plasmodium falciparum 3D7 Eplafa.cut
Proteus vulgaris Eprovu.cut
Pseudomonas aeruginosa PAO1 Epseae.cut
Pseudomonas putida KT2440 Epsepu.cut
Pseudomonas syringae pv tomato str DC3000 Epsesm.cut
Oryctolagus cuniculus (rabbit) Erabit.cut
Rattus norvegicus Erat.cut
Rhizobium leguminosarum Erhile.cut
Sinorhizobium meliloti 1021 Erhime.cut
Rhodobacter capsulatus Erhoca.cut
Rhodobacter sphaeroides Erhosh.cut
Salmo salar (Atlantic salmon) Esalsa.cut
Salmonella typhimurium LT2 Esalty.cut
Schistosoma mansoni Eschma.cut
Schizosaccharomyces pombe Eschpo.cut
Schizosaccharomyces pombe (CAI equivalent) Eschpo_cai.cut
Schizosaccharomyces pombe (high) Eschpo_high.cut
Serratia marcescens Eserma.cut
Ovis aries (sheep) Esheep.cut
Solanum tuberosum (potato) Esoltu.cut
Glycine max (soybean) Esoybn.cut
Spinacia oleracea (spinach) Espiol.cut
Staphylococcus aureus Estaau.cut
Streptomyces coelicolor A3 2 Estrco.cut
Streptococcus mutans UA159 Estrmu.cut
Streptococcus pneumoniae R6 Estrpn.cut
Strongylocentrotus purpuratus (sea urchin) Estrpu.cut
Simian Virus 40 Esv40.cut
Synechococcus sp WH 8102 Esynco.cut
Synechocystis sp PCC 6803 Esyncy.cut
Tetrahymena thermophila Etetth.cut
Thermus thermophilus HB8 Etheth.cut
Nicotiana tabacum (tobacco) Etobac.cut
Nicotiana tabacum chloroplast (tobacco) Etobac_chl.cut
Trypanosoma brucei Etrybr.cut
Trypanosoma cruzi Etrycr.cut
Vibrio cholerae O1 biovar eltor str N16961 Evibch.cut
Triticum aestivum (wheat) Ewheat.cut
Xenopus laevis Exenla.cut
Saccharomyces cerevisiae Eyeast.cut
Saccharomyces cerevisiae original CAI set Eyeast_cai.cut
Saccharomyces cerevisiae (high) Eyeast_high.cut
Saccharomyces cerevisiae mitochondrion Eyeast_mit.cut
Yersinia enterocolitica Eyeren.cut
Yersinia pestis Eyerpe.cut

Default value is: Homo sapiens [Ehuman.cut]

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
The EMBL-EBI bioinformatics web and programmatic tools framework.
(2015 Apr 06) Nucleic acids research
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