EMBOSS Backtranseq
Introduction
A program to back-translate a protein sequence to a nucleotide sequence.
- 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
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 | Etetpy.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).