|   | backtranambig | 
The resulting ambiguous nucleotide sequence can be translated to the original protein using transeq, which will recognise highly redundant codons (for example "WSN" for serine) as being produced by a program such as backtranambig.
| % backtranambig Back translate a protein sequence to ambiguous codons Input (gapped) protein sequence: tsw:opsd_human (gapped) nucleotide output sequence [opsd_human.fasta]: | 
Go to the input files for this example
Go to the output files for this example
| 
   Standard (Mandatory) qualifiers:
  [-sequence]          sequence   (Gapped) protein sequence filename and
                                  optional format, or reference (input USA)
  [-outfile]           seqout     [ | 
| Standard (Mandatory) qualifiers | Allowed values | Default | |||||||||||||||||||||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| [-sequence] (Parameter 1) | (Gapped) protein sequence filename and optional format, or reference (input USA) | Readable sequence | Required | ||||||||||||||||||||||||||||||||||||
| [-outfile] (Parameter 2) | (Gapped) nucleotide sequence filename and optional format (output USA) | Writeable sequence | <*>.format | ||||||||||||||||||||||||||||||||||||
| Additional (Optional) qualifiers | Allowed values | Default | |||||||||||||||||||||||||||||||||||||
| -table | Genetic code to use | 
 | 0 | ||||||||||||||||||||||||||||||||||||
| Advanced (Unprompted) qualifiers | Allowed values | Default | |||||||||||||||||||||||||||||||||||||
| (none) | |||||||||||||||||||||||||||||||||||||||
| 
ID   OPSD_HUMAN              Reviewed;         348 AA.
AC   P08100; Q16414; Q2M249;
DT   01-AUG-1988, integrated into UniProtKB/Swiss-Prot.
DT   01-AUG-1988, sequence version 1.
DT   20-MAR-2007, entry version 91.
DE   Rhodopsin (Opsin-2).
GN   Name=RHO; Synonyms=OPN2;
OS   Homo sapiens (Human).
OC   Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
OC   Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini;
OC   Catarrhini; Hominidae; Homo.
OX   NCBI_TaxID=9606;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RX   MEDLINE=84272729; PubMed=6589631;
RA   Nathans J., Hogness D.S.;
RT   "Isolation and nucleotide sequence of the gene encoding human
RT   rhodopsin.";
RL   Proc. Natl. Acad. Sci. U.S.A. 81:4851-4855(1984).
RN   [2]
RP   NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RA   Suwa M., Sato T., Okouchi I., Arita M., Futami K., Matsumoto S.,
RA   Tsutsumi S., Aburatani H., Asai K., Akiyama Y.;
RT   "Genome-wide discovery and analysis of human seven transmembrane helix
RT   receptor genes.";
RL   Submitted (JUL-2001) to the EMBL/GenBank/DDBJ databases.
RN   [3]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC   TISSUE=Retina;
RG   The German cDNA consortium;
RL   Submitted (JUN-2003) to the EMBL/GenBank/DDBJ databases.
RN   [4]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RX   PubMed=15489334; DOI=10.1101/gr.2596504;
RG   The MGC Project Team;
RT   "The status, quality, and expansion of the NIH full-length cDNA
RT   project: the Mammalian Gene Collection (MGC).";
RL   Genome Res. 14:2121-2127(2004).
RN   [5]
RP   NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-120.
RX   PubMed=8566799; DOI=10.1016/0378-1119(95)00688-5;
RA   Bennett J., Beller B., Sun D., Kariko K.;
RT   "Sequence analysis of the 5.34-kb 5' flanking region of the human
RT   rhodopsin-encoding gene.";
RL   Gene 167:317-320(1995).
RN   [6]
RP   REVIEW ON RP4 VARIANTS.
RX   MEDLINE=94004905; PubMed=8401533;
RA   Al-Maghtheh M., Gregory C., Inglehearn C., Hardcastle A.,
RA   Bhattacharya S.;
  [Part of this file has been deleted for brevity]
FT                                /FTId=VAR_004816.
FT   VARIANT     209    209       V -> M (effect not known).
FT                                /FTId=VAR_004817.
FT   VARIANT     211    211       H -> P (in RP4).
FT                                /FTId=VAR_004818.
FT   VARIANT     211    211       H -> R (in RP4).
FT                                /FTId=VAR_004819.
FT   VARIANT     216    216       M -> K (in RP4).
FT                                /FTId=VAR_004820.
FT   VARIANT     220    220       F -> C (in RP4).
FT                                /FTId=VAR_004821.
FT   VARIANT     222    222       C -> R (in RP4).
FT                                /FTId=VAR_004822.
FT   VARIANT     255    255       Missing (in RP4).
FT                                /FTId=VAR_004823.
FT   VARIANT     264    264       Missing (in RP4).
FT                                /FTId=VAR_004824.
FT   VARIANT     267    267       P -> L (in RP4).
FT                                /FTId=VAR_004825.
FT   VARIANT     267    267       P -> R (in RP4).
FT                                /FTId=VAR_004826.
FT   VARIANT     292    292       A -> E (in CSNBAD1).
FT                                /FTId=VAR_004827.
FT   VARIANT     296    296       K -> E (in RP4).
FT                                /FTId=VAR_004828.
FT   VARIANT     297    297       S -> R (in RP4).
FT                                /FTId=VAR_004829.
FT   VARIANT     342    342       T -> M (in RP4).
FT                                /FTId=VAR_004830.
FT   VARIANT     345    345       V -> L (in RP4).
FT                                /FTId=VAR_004831.
FT   VARIANT     345    345       V -> M (in RP4).
FT                                /FTId=VAR_004832.
FT   VARIANT     347    347       P -> A (in RP4).
FT                                /FTId=VAR_004833.
FT   VARIANT     347    347       P -> L (in RP4; common variant).
FT                                /FTId=VAR_004834.
FT   VARIANT     347    347       P -> Q (in RP4).
FT                                /FTId=VAR_004835.
FT   VARIANT     347    347       P -> R (in RP4).
FT                                /FTId=VAR_004836.
FT   VARIANT     347    347       P -> S (in RP4).
FT                                /FTId=VAR_004837.
SQ   SEQUENCE   348 AA;  38893 MW;  6F4F6FCBA34265B2 CRC64;
     MNGTEGPNFY VPFSNATGVV RSPFEYPQYY LAEPWQFSML AAYMFLLIVL GFPINFLTLY
     VTVQHKKLRT PLNYILLNLA VADLFMVLGG FTSTLYTSLH GYFVFGPTGC NLEGFFATLG
     GEIALWSLVV LAIERYVVVC KPMSNFRFGE NHAIMGVAFT WVMALACAAP PLAGWSRYIP
     EGLQCSCGID YYTLKPEVNN ESFVIYMFVV HFTIPMIIIF FCYGQLVFTV KEAAAQQQES
     ATTQKAEKEV TRMVIIMVIA FLICWVPYAS VAFYIFTHQG SNFGPIFMTI PAFFAKSAAI
     YNPVIYIMMN KQFRNCMLTT ICCGKNPLGD DEASATVSKT ETSQVAPA
//
 | 
| >OPSD_HUMAN P08100 Rhodopsin (Opsin-2). ATGAAYGGNACNGARGGNCCNAAYTTYTAYGTNCCNTTYWSNAAYGCNACNGGNGTNGTN MGNWSNCCNTTYGARTAYCCNCARTAYTAYYTNGCNGARCCNTGGCARTTYWSNATGYTN GCNGCNTAYATGTTYYTNYTNATHGTNYTNGGNTTYCCNATHAAYTTYYTNACNYTNTAY GTNACNGTNCARCAYAARAARYTNMGNACNCCNYTNAAYTAYATHYTNYTNAAYYTNGCN GTNGCNGAYYTNTTYATGGTNYTNGGNGGNTTYACNWSNACNYTNTAYACNWSNYTNCAY GGNTAYTTYGTNTTYGGNCCNACNGGNTGYAAYYTNGARGGNTTYTTYGCNACNYTNGGN GGNGARATHGCNYTNTGGWSNYTNGTNGTNYTNGCNATHGARMGNTAYGTNGTNGTNTGY AARCCNATGWSNAAYTTYMGNTTYGGNGARAAYCAYGCNATHATGGGNGTNGCNTTYACN TGGGTNATGGCNYTNGCNTGYGCNGCNCCNCCNYTNGCNGGNTGGWSNMGNTAYATHCCN GARGGNYTNCARTGYWSNTGYGGNATHGAYTAYTAYACNYTNAARCCNGARGTNAAYAAY GARWSNTTYGTNATHTAYATGTTYGTNGTNCAYTTYACNATHCCNATGATHATHATHTTY TTYTGYTAYGGNCARYTNGTNTTYACNGTNAARGARGCNGCNGCNCARCARCARGARWSN GCNACNACNCARAARGCNGARAARGARGTNACNMGNATGGTNATHATHATGGTNATHGCN TTYYTNATHTGYTGGGTNCCNTAYGCNWSNGTNGCNTTYTAYATHTTYACNCAYCARGGN WSNAAYTTYGGNCCNATHTTYATGACNATHCCNGCNTTYTTYGCNAARWSNGCNGCNATH TAYAAYCCNGTNATHTAYATHATGATGAAYAARCARTTYMGNAAYTGYATGYTNACNACN ATHTGYTGYGGNAARAAYCCNYTNGGNGAYGAYGARGCNWSNGCNACNGTNWSNAARACN GARACNWSNCARGTNGCNCCNGCN | 
EMBOSS data files are distributed with the application and stored in the standard EMBOSS data directory, which is defined by the EMBOSS environment variable EMBOSS_DATA.
To see the available EMBOSS data files, run:
% embossdata -showall
To fetch one of the data files (for example 'Exxx.dat') into your current directory for you to inspect or modify, run:
% embossdata -fetch -file Exxx.dat
Users can provide their own data files in their own directories. Project specific files can be put in the current directory, or for tidier directory listings in a subdirectory called ".embossdata". Files for all EMBOSS runs can be put in the user's home directory, or again in a subdirectory called ".embossdata".
The directories are searched in the following order:
"The file 'drosoph.cut' does not exist" - the codon usage file cannot be opened.
| Program name | Description | 
|---|---|
| backtranseq | Back translate a protein sequence | 
| charge | Protein charge plot | 
| checktrans | Reports STOP codons and ORF statistics of a protein | 
| coderet | Extract CDS, mRNA and translations from feature tables | 
| compseq | Count composition of dimer/trimer/etc words in a sequence | 
| emowse | Protein identification by mass spectrometry | 
| freak | Residue/base frequency table or plot | 
| iep | Calculates the isoelectric point of a protein | 
| mwcontam | Shows molwts that match across a set of files | 
| mwfilter | Filter noisy molwts from mass spec output | 
| octanol | Displays protein hydropathy | 
| pepinfo | Plots simple amino acid properties in parallel | 
| pepstats | Protein statistics | 
| pepwindow | Displays protein hydropathy | 
| pepwindowall | Displays protein hydropathy of a set of sequences | 
| plotorf | Plot potential open reading frames | 
| prettyseq | Output sequence with translated ranges | 
| remap | Display sequence with restriction sites, translation etc | 
| showorf | Pretty output of DNA translations | 
| showseq | Display a sequence with features, translation etc | 
| sixpack | Display a DNA sequence with 6-frame translation and ORFs | 
| transeq | Translate nucleic acid sequences |