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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 | |||||||||||||||||||||||||||||||||||||
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[-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 | |||||||||||||||||||||||||||||||||||||
Additional (Optional) qualifiers | Allowed values | Default | |||||||||||||||||||||||||||||||||||||
-table | Genetic code to use |
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0 | ||||||||||||||||||||||||||||||||||||
Advanced (Unprompted) qualifiers | Allowed values | Default | |||||||||||||||||||||||||||||||||||||
(none) |
ID OPSD_HUMAN STANDARD; PRT; 348 AA. AC P08100; Q16414; DT 01-AUG-1988 (Rel. 08, Created) DT 01-AUG-1988 (Rel. 08, Last sequence update) DT 15-JUL-1999 (Rel. 38, Last annotation update) DE RHODOPSIN. GN RHO. OS Homo sapiens (Human). OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Mammalia; OC Eutheria; Primates; Catarrhini; Hominidae; Homo. RN [1] RP SEQUENCE FROM N.A. RX MEDLINE; 84272729. 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 SEQUENCE OF 1-120 FROM N.A. RA BENNETT J., BELLER B., SUN D., KARIKO K.; RL Submitted (NOV-1994) to the EMBL/GenBank/DDBJ databases. RN [3] RP REVIEW ON ADRP VARIANTS. RX MEDLINE; 94004905. RA AL-MAGHTHEH M., GREGORY C., INGLEHEARN C., HARDCASTLE A., RA BHATTACHARYA S.; RT "Rhodopsin mutations in autosomal dominant retinitis pigmentosa."; RL Hum. Mutat. 2:249-255(1993). RN [4] RP VARIANT ADRP HIS-23. RX MEDLINE; 90136922. RA DRYJA T.P., MCGEE T.L., REICHEI E., HAHN L.B., COWLEY G.S., RA YANDELL D.W., SANDBERG M.A., BERSON E.L.; RT "A point mutation of the rhodopsin gene in one form of retinitis RT pigmentosa."; RL Nature 343:364-366(1990). RN [5] RP VARIANTS ADRP. RX MEDLINE; 91051574. RA FARRAR G.J., KENNA P., REDMOND R., MCWILLIAM P., BRADLEY D.G., RA HUMPHRIES M.M., SHARP E.M., INGLEHEARN C.F., BASHIR R., JAY M., RA WATTY A., LUDWIG M., SCHINZEL A., SAMANNS C., GAL A., RA BHATTACHARYA S.S., HUMPHRIES P.; RT "Autosomal dominant retinitis pigmentosa: absence of the rhodopsin RT proline-->histidine substitution (codon 23) in pedigrees from RT Europe."; RL Am. J. Hum. Genet. 47:941-945(1990). RN [6] RP VARIANTS ADRP HIS-23; ARG-58; LEU-347 AND SER-347. RX MEDLINE; 91015273. [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 ADRP). FT /FTId=VAR_004818. FT VARIANT 211 211 H -> R (IN ADRP). FT /FTId=VAR_004819. FT VARIANT 216 216 M -> K (IN ADRP). FT /FTId=VAR_004820. FT VARIANT 220 220 F -> C (IN ADRP). FT /FTId=VAR_004821. FT VARIANT 222 222 C -> R (IN ADRP). FT /FTId=VAR_004822. FT VARIANT 255 255 MISSING (IN ADRP). FT /FTId=VAR_004823. FT VARIANT 264 264 MISSING (IN ADRP). FT /FTId=VAR_004824. FT VARIANT 267 267 P -> L (IN ADRP). FT /FTId=VAR_004825. FT VARIANT 267 267 P -> R (IN ADRP). FT /FTId=VAR_004826. FT VARIANT 292 292 A -> E (IN CSNB4). FT /FTId=VAR_004827. FT VARIANT 296 296 K -> E (IN ADRP). FT /FTId=VAR_004828. FT VARIANT 297 297 S -> R (IN ADRP). FT /FTId=VAR_004829. FT VARIANT 342 342 T -> M (IN ADRP). FT /FTId=VAR_004830. FT VARIANT 345 345 V -> L (IN ADRP). FT /FTId=VAR_004831. FT VARIANT 345 345 V -> M (IN ADRP). FT /FTId=VAR_004832. FT VARIANT 347 347 P -> A (IN ADRP). FT /FTId=VAR_004833. FT VARIANT 347 347 P -> L (IN ADRP; COMMON VARIANT). FT /FTId=VAR_004834. FT VARIANT 347 347 P -> Q (IN ADRP). FT /FTId=VAR_004835. FT VARIANT 347 347 P -> R (IN ADRP). FT /FTId=VAR_004836. FT VARIANT 347 347 P -> S (IN ADRP). FT /FTId=VAR_004837. SQ SEQUENCE 348 AA; 38892 MW; 07443BEA CRC32; 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. 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 |