backtranambig |
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backtranambig reads a protein sequence and writes the nucleic acid sequence it could have come from. It does this by using nucleotide ambiguity codes that represent all possible codons for each amino acid.
backtranambig needs a genetic code to generate an ambiguous codon for each amino acid. The default genetic code is the standard ("Universal") code, although many others are available via the '-table' qualifier. The codon usage tables correspdonding to these codes must exist in the EMBOSS data directory. See the section on "Data Files" below for more information.
% backtranambig Back-translate a protein sequence to ambiguous nucleotide sequence Input (gapped) protein sequence(s): tsw:opsd_human (gapped) nucleotide output sequence(s) [opsd_human.fasta]: |
Go to the input files for this example
Go to the output files for this example
Back-translate a protein sequence to ambiguous nucleotide sequence Version: EMBOSS:6.6.0.0 Standard (Mandatory) qualifiers: [-sequence] seqall (Gapped) protein sequence(s) filename and optional format, or reference (input USA) [-outfile] seqoutall [ |
Qualifier | Type | Description | Allowed values | Default | ||||||||||||||||||||||||||||||||||||
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Standard (Mandatory) qualifiers | ||||||||||||||||||||||||||||||||||||||||
[-sequence] (Parameter 1) |
seqall | (Gapped) protein sequence(s) filename and optional format, or reference (input USA) | Readable sequence(s) | Required | ||||||||||||||||||||||||||||||||||||
[-outfile] (Parameter 2) |
seqoutall | (Aligned) nucleotide sequence set(s) filename and optional format (output USA) | Writeable sequence(s) | <*>.format | ||||||||||||||||||||||||||||||||||||
Additional (Optional) qualifiers | ||||||||||||||||||||||||||||||||||||||||
-table | list | Genetic code to use |
|
0 | ||||||||||||||||||||||||||||||||||||
Advanced (Unprompted) qualifiers | ||||||||||||||||||||||||||||||||||||||||
(none) | ||||||||||||||||||||||||||||||||||||||||
Associated qualifiers | ||||||||||||||||||||||||||||||||||||||||
"-sequence" associated seqall qualifiers | ||||||||||||||||||||||||||||||||||||||||
-sbegin1 -sbegin_sequence |
integer | Start of each sequence to be used | Any integer value | 0 | ||||||||||||||||||||||||||||||||||||
-send1 -send_sequence |
integer | End of each sequence to be used | Any integer value | 0 | ||||||||||||||||||||||||||||||||||||
-sreverse1 -sreverse_sequence |
boolean | Reverse (if DNA) | Boolean value Yes/No | N | ||||||||||||||||||||||||||||||||||||
-sask1 -sask_sequence |
boolean | Ask for begin/end/reverse | Boolean value Yes/No | N | ||||||||||||||||||||||||||||||||||||
-snucleotide1 -snucleotide_sequence |
boolean | Sequence is nucleotide | Boolean value Yes/No | N | ||||||||||||||||||||||||||||||||||||
-sprotein1 -sprotein_sequence |
boolean | Sequence is protein | Boolean value Yes/No | N | ||||||||||||||||||||||||||||||||||||
-slower1 -slower_sequence |
boolean | Make lower case | Boolean value Yes/No | N | ||||||||||||||||||||||||||||||||||||
-supper1 -supper_sequence |
boolean | Make upper case | Boolean value Yes/No | N | ||||||||||||||||||||||||||||||||||||
-scircular1 -scircular_sequence |
boolean | Sequence is circular | Boolean value Yes/No | N | ||||||||||||||||||||||||||||||||||||
-squick1 -squick_sequence |
boolean | Read id and sequence only | Boolean value Yes/No | N | ||||||||||||||||||||||||||||||||||||
-sformat1 -sformat_sequence |
string | Input sequence format | Any string | |||||||||||||||||||||||||||||||||||||
-iquery1 -iquery_sequence |
string | Input query fields or ID list | Any string | |||||||||||||||||||||||||||||||||||||
-ioffset1 -ioffset_sequence |
integer | Input start position offset | Any integer value | 0 | ||||||||||||||||||||||||||||||||||||
-sdbname1 -sdbname_sequence |
string | Database name | Any string | |||||||||||||||||||||||||||||||||||||
-sid1 -sid_sequence |
string | Entryname | Any string | |||||||||||||||||||||||||||||||||||||
-ufo1 -ufo_sequence |
string | UFO features | Any string | |||||||||||||||||||||||||||||||||||||
-fformat1 -fformat_sequence |
string | Features format | Any string | |||||||||||||||||||||||||||||||||||||
-fopenfile1 -fopenfile_sequence |
string | Features file name | Any string | |||||||||||||||||||||||||||||||||||||
"-outfile" associated seqoutall qualifiers | ||||||||||||||||||||||||||||||||||||||||
-osformat2 -osformat_outfile |
string | Output seq format | Any string | |||||||||||||||||||||||||||||||||||||
-osextension2 -osextension_outfile |
string | File name extension | Any string | |||||||||||||||||||||||||||||||||||||
-osname2 -osname_outfile |
string | Base file name | Any string | |||||||||||||||||||||||||||||||||||||
-osdirectory2 -osdirectory_outfile |
string | Output directory | Any string | |||||||||||||||||||||||||||||||||||||
-osdbname2 -osdbname_outfile |
string | Database name to add | Any string | |||||||||||||||||||||||||||||||||||||
-ossingle2 -ossingle_outfile |
boolean | Separate file for each entry | Boolean value Yes/No | N | ||||||||||||||||||||||||||||||||||||
-oufo2 -oufo_outfile |
string | UFO features | Any string | |||||||||||||||||||||||||||||||||||||
-offormat2 -offormat_outfile |
string | Features format | Any string | |||||||||||||||||||||||||||||||||||||
-ofname2 -ofname_outfile |
string | Features file name | Any string | |||||||||||||||||||||||||||||||||||||
-ofdirectory2 -ofdirectory_outfile |
string | Output directory | Any string | |||||||||||||||||||||||||||||||||||||
General qualifiers | ||||||||||||||||||||||||||||||||||||||||
-auto | boolean | Turn off prompts | Boolean value Yes/No | N | ||||||||||||||||||||||||||||||||||||
-stdout | boolean | Write first file to standard output | Boolean value Yes/No | N | ||||||||||||||||||||||||||||||||||||
-filter | boolean | Read first file from standard input, write first file to standard output | Boolean value Yes/No | N | ||||||||||||||||||||||||||||||||||||
-options | boolean | Prompt for standard and additional values | Boolean value Yes/No | N | ||||||||||||||||||||||||||||||||||||
-debug | boolean | Write debug output to program.dbg | Boolean value Yes/No | N | ||||||||||||||||||||||||||||||||||||
-verbose | boolean | Report some/full command line options | Boolean value Yes/No | Y | ||||||||||||||||||||||||||||||||||||
-help | boolean | Report command line options and exit. More information on associated and general qualifiers can be found with -help -verbose | Boolean value Yes/No | N | ||||||||||||||||||||||||||||||||||||
-warning | boolean | Report warnings | Boolean value Yes/No | Y | ||||||||||||||||||||||||||||||||||||
-error | boolean | Report errors | Boolean value Yes/No | Y | ||||||||||||||||||||||||||||||||||||
-fatal | boolean | Report fatal errors | Boolean value Yes/No | Y | ||||||||||||||||||||||||||||||||||||
-die | boolean | Report dying program messages | Boolean value Yes/No | Y | ||||||||||||||||||||||||||||||||||||
-version | boolean | Report version number and exit | Boolean value Yes/No | N |
The input is a standard EMBOSS sequence query (also known as a 'USA').
Major sequence database sources defined as standard in EMBOSS installations include srs:embl, srs:uniprot and ensembl
Data can also be read from sequence output in any supported format written by an EMBOSS or third-party application.
The input format can be specified by using the command-line qualifier -sformat xxx, where 'xxx' is replaced by the name of the required format. The available format names are: gff (gff3), gff2, embl (em), genbank (gb, refseq), ddbj, refseqp, pir (nbrf), swissprot (swiss, sw), dasgff and debug.
See: http://emboss.sf.net/docs/themes/SequenceFormats.html for further information on sequence formats.
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 13-JUN-2012, entry version 145. DE RecName: Full=Rhodopsin; DE AltName: Full=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; DOI=10.1073/pnas.81.15.4851; 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; RX PubMed=17974005; DOI=10.1186/1471-2164-8-399; RA Bechtel S., Rosenfelder H., Duda A., Schmidt C.P., Ernst U., RA Wellenreuther R., Mehrle A., Schuster C., Bahr A., Bloecker H., RA Heubner D., Hoerlein A., Michel G., Wedler H., Koehrer K., RA Ottenwaelder B., Poustka A., Wiemann S., Schupp I.; RT "The full-ORF clone resource of the German cDNA consortium."; RL BMC Genomics 8:399-399(2007). 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."; [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; dbSNP:rs28933993). 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; dbSNP:rs29001653). 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; dbSNP:rs29001566). FT /FTId=VAR_004836. FT VARIANT 347 347 P -> S (in RP4; dbSNP:rs29001637). 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 // |
The output is a standard EMBOSS sequence file.
The results can be output in one of several styles by using the command-line qualifier -osformat xxx, where 'xxx' is replaced by the name of the required format. The available format names are: embl, genbank, gff, pir, swiss, dasgff, debug, listfile, dbmotif, diffseq, excel, feattable, motif, nametable, regions, seqtable, simple, srs, table, tagseq.
See: http://emboss.sf.net/docs/themes/SequenceFormats.html for further information on sequence formats.
>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 ambiguous nucleotide sequence generated by backtranambig 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.
"The file 'drosoph.cut' does not exist" - the codon usage file cannot be opened.
Program name | Description |
---|---|
backtranseq | Back-translate a protein sequence to a nucleotide sequence |
checktrans | Report 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 |
mwcontam | Find weights common to multiple molecular weights files |
mwfilter | Filter noisy data from molecular weights file |
oddcomp | Identify proteins with specified sequence word composition |
pepdigest | Report on protein proteolytic enzyme or reagent cleavage sites |
pepinfo | Plot amino acid properties of a protein sequence in parallel |
pepstats | Calculate statistics of protein properties |
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 | Display 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 molecular sequence(s) |
Please report all bugs to the EMBOSS bug team (emboss-bug © emboss.open-bio.org) not to the original author.