backtranseq |
backtranseq reads a protein sequence and writes the nucleic acid sequence it is most likely to have come from.
backtranseq uses a codon usage table which gives the frequency of usage of each codon for each amino acid. For each amino acid in the input sequence, the corresponding most frequently occuring codon is used in the nucleic acid sequence that is output.
Note that this is a human protein and so the default human codon frequency file is used ie. is not specified
% backtranseq Back-translate a protein sequence to a nucleotide sequence 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
Example 2
This uses a drosophila sequence and codon table.
% backtranseq -cfile Edrome.cut Back-translate a protein sequence to a nucleotide sequence Input (gapped) protein sequence: tsw:ach2_drome (gapped) nucleotide output sequence [ach2_drome.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 | |
-cfile | Codon usage table name | Codon usage file in EMBOSS data path | Ehuman.cut |
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 // |
ID ACH2_DROME Reviewed; 576 AA. AC P17644; Q9VC73; DT 01-AUG-1990, integrated into UniProtKB/Swiss-Prot. DT 01-AUG-1990, sequence version 1. DT 03-APR-2007, entry version 78. DE Acetylcholine receptor subunit alpha-like 2 precursor. GN Name=nAcR-alpha-96Ab; Synonyms=Acr96Ab, AcrE, sad; ORFNames=CG6844; OS Drosophila melanogaster (Fruit fly). OC Eukaryota; Metazoa; Arthropoda; Hexapoda; Insecta; Pterygota; OC Neoptera; Endopterygota; Diptera; Brachycera; Muscomorpha; OC Ephydroidea; Drosophilidae; Drosophila. OX NCBI_TaxID=7227; RN [1] RP NUCLEOTIDE SEQUENCE [MRNA]. RC TISSUE=Head; RX MEDLINE=90301489; PubMed=2114015; DOI=10.1093/nar/18.12.3640; RA Baumann A., Jonas P., Gundelfinger E.D.; RT "Sequence of D alpha 2, a novel alpha-like subunit of Drosophila RT nicotinic acetylcholine receptors."; RL Nucleic Acids Res. 18:3640-3640(1990). RN [2] RP NUCLEOTIDE SEQUENCE [GENOMIC DNA]. RC TISSUE=Head; RX MEDLINE=90353591; PubMed=2117557; DOI=10.1016/0014-5793(90)81170-S; RA Jonas P., Baumann A., Merz B., Gundelfinger E.D.; RT "Structure and developmental expression of the D alpha 2 gene encoding RT a novel nicotinic acetylcholine receptor protein of Drosophila RT melanogaster."; RL FEBS Lett. 269:264-268(1990). RN [3] RP NUCLEOTIDE SEQUENCE [MRNA]. RX MEDLINE=90360975; PubMed=1697262; RA Sawruk E., Schloss P., Betz H., Schmitt B.; RT "Heterogeneity of Drosophila nicotinic acetylcholine receptors: SAD, a RT novel developmentally regulated alpha-subunit."; RL EMBO J. 9:2671-2677(1990). RN [4] RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. RC STRAIN=Berkeley; RX MEDLINE=20196006; PubMed=10731132; DOI=10.1126/science.287.5461.2185; RA Adams M.D., Celniker S.E., Holt R.A., Evans C.A., Gocayne J.D., RA Amanatides P.G., Scherer S.E., Li P.W., Hoskins R.A., Galle R.F., RA George R.A., Lewis S.E., Richards S., Ashburner M., Henderson S.N., RA Sutton G.G., Wortman J.R., Yandell M.D., Zhang Q., Chen L.X., RA Brandon R.C., Rogers Y.-H.C., Blazej R.G., Champe M., Pfeiffer B.D., RA Wan K.H., Doyle C., Baxter E.G., Helt G., Nelson C.R., Miklos G.L.G., RA Abril J.F., Agbayani A., An H.-J., Andrews-Pfannkoch C., Baldwin D., RA Ballew R.M., Basu A., Baxendale J., Bayraktaroglu L., Beasley E.M., RA Beeson K.Y., Benos P.V., Berman B.P., Bhandari D., Bolshakov S., RA Borkova D., Botchan M.R., Bouck J., Brokstein P., Brottier P., [Part of this file has been deleted for brevity] DR IntAct; P17644; -. DR Ensembl; CG6844; Drosophila melanogaster. DR KEGG; dme:Dmel_CG6844; -. DR FlyBase; FBgn0000039; nAcR-alpha-96Ab. DR BioCyc; DMEL-XXX-02:DMEL-XXX-02-013190-MONOMER; -. DR BioCyc; DMEL-XXX-02:DMEL-XXX-02-013191-MONOMER; -. DR GermOnline; CG6844; Drosophila melanogaster. DR GO; GO:0005515; F:protein binding; IPI:IntAct. DR InterPro; IPR006029; Neu_channel_TM. DR InterPro; IPR006202; Neur_chan_lig_bd. DR InterPro; IPR006201; Neur_channel. DR InterPro; IPR002394; Nic_ach_rcpt. DR Gene3D; G3DSA:3.30.1100.20; Neur_chan_lig_bd; 1. DR PANTHER; PTHR18945; Neur_channel; 2. DR Pfam; PF02931; Neur_chan_LBD; 1. DR Pfam; PF02932; Neur_chan_memb; 1. DR PRINTS; PR00254; NICOTINICR. DR PRINTS; PR00252; NRIONCHANNEL. DR TIGRFAMs; TIGR00860; LIC; 1. DR PROSITE; PS00236; NEUROTR_ION_CHANNEL; 1. KW Complete proteome; Glycoprotein; Ion transport; Ionic channel; KW Membrane; Postsynaptic membrane; Receptor; Signal; Transmembrane; KW Transport. FT SIGNAL 1 21 Probable. FT CHAIN 22 576 Acetylcholine receptor subunit alpha-like FT 2. FT /FTId=PRO_0000000300. FT TOPO_DOM 22 261 Extracellular (Potential). FT TRANSMEM 262 285 Potential. FT TRANSMEM 293 311 Potential. FT TRANSMEM 327 346 Potential. FT TOPO_DOM 347 526 Cytoplasmic (Potential). FT TRANSMEM 527 545 Potential. FT CARBOHYD 65 65 N-linked (GlcNAc...) (Potential). FT CARBOHYD 254 254 N-linked (GlcNAc...) (Potential). FT CARBOHYD 570 570 N-linked (GlcNAc...) (Potential). FT DISULFID 169 183 By similarity. FT DISULFID 243 244 Associated with receptor activation (By FT similarity). SQ SEQUENCE 576 AA; 65506 MW; 97D6A46CADC3F42F CRC64; MAPGCCTTRP RPIALLAHIW RHCKPLCLLL VLLLLCETVQ ANPDAKRLYD DLLSNYNRLI RPVSNNTDTV LVKLGLRLSQ LIDLNLKDQI LTTNVWLEHE WQDHKFKWDP SEYGGVTELY VPSEHIWLPD IVLYNNADGE YVVTTMTKAI LHYTGKVVWT PPAIFKSSCE IDVRYFPFDQ QTCFMKFGSW TYDGDQIDLK HISQKNDKDN KVEIGIDLRE YYPSVEWDIL GVPAERHEKY YPCCAEPYPD IFFNITLRRK TLFYTVNLII PCVGISYLSV LVFYLPADSG EKIALCISIL LSQTMFFLLI SEIIPSTSLA LPLLGKYLLF TMLLVGLSVV ITIIILNIHY RKPSTHKMRP WIRSFFIKRL PKLLLMRVPK DLLRDLAANK INYGLKFSKT KFGQALMDEM QMNSGGSSPD SLRRMQGRVG AGGCNGMHVT TATNRFSGLV GALGGGLSTL SGYNGLPSVL SGLDDSLSDV AARKKYPFEL EKAIHNVMFI QHHMQRQDEF NAEDQDWGFV AMVMDRLFLW LFMIASLVGT FVILGEAPSL YDDTKAIDVQ LSDVAKQIYN LTEKKN // |
>OPSD_HUMAN P08100 Rhodopsin (Opsin-2). ATGAACGGCACCGAGGGCCCCAACTTCTACGTGCCCTTCAGCAACGCCACCGGCGTGGTG AGGAGCCCCTTCGAGTACCCCCAGTACTACCTGGCCGAGCCCTGGCAGTTCAGCATGCTG GCCGCCTACATGTTCCTGCTGATCGTGCTGGGCTTCCCCATCAACTTCCTGACCCTGTAC GTGACCGTGCAGCACAAGAAGCTGAGGACCCCCCTGAACTACATCCTGCTGAACCTGGCC GTGGCCGACCTGTTCATGGTGCTGGGCGGCTTCACCAGCACCCTGTACACCAGCCTGCAC GGCTACTTCGTGTTCGGCCCCACCGGCTGCAACCTGGAGGGCTTCTTCGCCACCCTGGGC GGCGAGATCGCCCTGTGGAGCCTGGTGGTGCTGGCCATCGAGAGGTACGTGGTGGTGTGC AAGCCCATGAGCAACTTCAGGTTCGGCGAGAACCACGCCATCATGGGCGTGGCCTTCACC TGGGTGATGGCCCTGGCCTGCGCCGCCCCCCCCCTGGCCGGCTGGAGCAGGTACATCCCC GAGGGCCTGCAGTGCAGCTGCGGCATCGACTACTACACCCTGAAGCCCGAGGTGAACAAC GAGAGCTTCGTGATCTACATGTTCGTGGTGCACTTCACCATCCCCATGATCATCATCTTC TTCTGCTACGGCCAGCTGGTGTTCACCGTGAAGGAGGCCGCCGCCCAGCAGCAGGAGAGC GCCACCACCCAGAAGGCCGAGAAGGAGGTGACCAGGATGGTGATCATCATGGTGATCGCC TTCCTGATCTGCTGGGTGCCCTACGCCAGCGTGGCCTTCTACATCTTCACCCACCAGGGC AGCAACTTCGGCCCCATCTTCATGACCATCCCCGCCTTCTTCGCCAAGAGCGCCGCCATC TACAACCCCGTGATCTACATCATGATGAACAAGCAGTTCAGGAACTGCATGCTGACCACC ATCTGCTGCGGCAAGAACCCCCTGGGCGACGACGAGGCCAGCGCCACCGTGAGCAAGACC GAGACCAGCCAGGTGGCCCCCGCC |
>ACH2_DROME P17644 Acetylcholine receptor subunit alpha-like 2 precursor. ATGGCCCCCGGCTGCTGCACCACCCGCCCCCGCCCCATCGCCCTGCTGGCCCACATCTGG CGCCACTGCAAGCCCCTGTGCCTGCTGCTGGTGCTGCTGCTGCTGTGCGAGACCGTGCAG GCCAACCCCGATGCCAAGCGCCTGTACGATGATCTGCTGAGCAACTACAACCGCCTGATC CGCCCCGTGAGCAACAACACCGATACCGTGCTGGTGAAGCTGGGCCTGCGCCTGAGCCAG CTGATCGATCTGAACCTGAAGGATCAGATCCTGACCACCAACGTGTGGCTGGAGCACGAG TGGCAGGATCACAAGTTCAAGTGGGATCCCAGCGAGTACGGCGGCGTGACCGAGCTGTAC GTGCCCAGCGAGCACATCTGGCTGCCCGATATCGTGCTGTACAACAACGCCGATGGCGAG TACGTGGTGACCACCATGACCAAGGCCATCCTGCACTACACCGGCAAGGTGGTGTGGACC CCCCCCGCCATCTTCAAGAGCAGCTGCGAGATCGATGTGCGCTACTTCCCCTTCGATCAG CAGACCTGCTTCATGAAGTTCGGCAGCTGGACCTACGATGGCGATCAGATCGATCTGAAG CACATCAGCCAGAAGAACGATAAGGATAACAAGGTGGAGATCGGCATCGATCTGCGCGAG TACTACCCCAGCGTGGAGTGGGATATCCTGGGCGTGCCCGCCGAGCGCCACGAGAAGTAC TACCCCTGCTGCGCCGAGCCCTACCCCGATATCTTCTTCAACATCACCCTGCGCCGCAAG ACCCTGTTCTACACCGTGAACCTGATCATCCCCTGCGTGGGCATCAGCTACCTGAGCGTG CTGGTGTTCTACCTGCCCGCCGATAGCGGCGAGAAGATCGCCCTGTGCATCAGCATCCTG CTGAGCCAGACCATGTTCTTCCTGCTGATCAGCGAGATCATCCCCAGCACCAGCCTGGCC CTGCCCCTGCTGGGCAAGTACCTGCTGTTCACCATGCTGCTGGTGGGCCTGAGCGTGGTG ATCACCATCATCATCCTGAACATCCACTACCGCAAGCCCAGCACCCACAAGATGCGCCCC TGGATCCGCAGCTTCTTCATCAAGCGCCTGCCCAAGCTGCTGCTGATGCGCGTGCCCAAG GATCTGCTGCGCGATCTGGCCGCCAACAAGATCAACTACGGCCTGAAGTTCAGCAAGACC AAGTTCGGCCAGGCCCTGATGGATGAGATGCAGATGAACAGCGGCGGCAGCAGCCCCGAT AGCCTGCGCCGCATGCAGGGCCGCGTGGGCGCCGGCGGCTGCAACGGCATGCACGTGACC ACCGCCACCAACCGCTTCAGCGGCCTGGTGGGCGCCCTGGGCGGCGGCCTGAGCACCCTG AGCGGCTACAACGGCCTGCCCAGCGTGCTGAGCGGCCTGGATGATAGCCTGAGCGATGTG GCCGCCCGCAAGAAGTACCCCTTCGAGCTGGAGAAGGCCATCCACAACGTGATGTTCATC CAGCACCACATGCAGCGCCAGGATGAGTTCAACGCCGAGGATCAGGATTGGGGCTTCGTG GCCATGGTGATGGATCGCCTGTTCCTGTGGCTGTTCATGATCGCCAGCCTGGTGGGCACC TTCGTGATCCTGGGCGAGGCCCCCAGCCTGTACGATGATACCAAGGCCATCGATGTGCAG CTGAGCGATGTGGCCAAGCAGATCTACAACCTGACCGAGAAGAAGAAC |
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:
backtranseq reads a data file containing the codon usage table. The default file is Ehum.cut - the human codon usage table. Many others are available and can be set by name with the -cfile qualifier. It is important to use one that is appropriate for the species that your protein comes from. The specified data file must exist in the EMBOSS data directory (see below for more information).
"The file 'drosoph.cut' does not exist" - the codon usage file cannot be opened.
Program name | Description |
---|---|
backtranambig | Back-translate a protein sequence to ambiguous nucleotide sequence |
charge | Draw a protein charge plot |
checktrans | Reports STOP codons and ORF statistics of a protein |
coderet | Extract CDS, mRNA and translations from feature tables |
compseq | Calculate the composition of unique words in sequences |
emowse | Search protein sequences by digest fragment molecular weight |
freak | Generate residue/base frequency table or plot |
iep | Calculate the isoelectric point of proteins |
mwcontam | Find weights common to multiple molecular weights files |
mwfilter | Filter noisy data from molecular weights file |
octanol | Draw a White-Wimley protein hydropathy plot |
pepinfo | Plot amino acid properties of a protein sequence in parallel |
pepstats | Calculates statistics of protein properties |
pepwindow | Draw a Kyte-Doolittle hydropathy plot for a protein sequence |
pepwindowall | Draw Kyte-Doolittle hydropathy plot for a protein alignment |
plotorf | Plot potential open reading frames in a nucleotide sequence |
prettyseq | Write a nucleotide sequence and its translation to file |
remap | Display restriction enzyme binding sites in a nucleotide sequence |
showorf | Display a nucleotide sequence and translation in pretty format |
showseq | Displays sequences with features in pretty format |
sixpack | Display a DNA sequence with 6-frame translation and ORFs |
transeq | Translate nucleic acid sequences |
wordcount | Count and extract unique words in DNA sequence(s) |