Appdoc:Backtranambig

From EMBOSS

Contents 1 Function 2 Description 3 Algorithm 4 Usage 5 Command line arguments 6 Input file format 6.1 Input example 6.1.1 Database entry: tsw:opsd_human 7 Output file format 7.1 Output example 7.1.1 File: opsd_human.fasta 8 Data files 9 Notes 10 References 11 Warnings 12 Diagnostic Error Messages 13 Exit status 14 Known bugs 15 See also 16 Author(s) 17 History 18 Target users 19 Comments

Function

Back-translate a protein sequence to ambiguous nucleotide sequence

Description

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.

Algorithm

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.

Usage

Here is a sample session with backtranambig

% 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

Command line arguments

Qualifier	Type	Description	Allowed values	Default
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	(Standard)
1	(Standard (with alternative initiation codons))
2	(Vertebrate Mitochondrial)
3	(Yeast Mitochondrial)
4	(Mold, Protozoan, Coelenterate Mitochondrial and Mycoplasma/Spiroplasma)
5	(Invertebrate Mitochondrial)
6	(Ciliate Macronuclear and Dasycladacean)
9	(Echinoderm Mitochondrial)
10	(Euplotid Nuclear)
11	(Bacterial)
12	(Alternative Yeast Nuclear)
13	(Ascidian Mitochondrial)
14	(Flatworm Mitochondrial)
15	(Blepharisma Macronuclear)
16	(Chlorophycean Mitochondrial)
21	(Trematode Mitochondrial)
22	(Scenedesmus obliquus)
23	(Thraustochytrium Mitochondrial)	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
-sformat1 -sformat_sequence	string	Input sequence format	Any string
-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. 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

Input file format

Any DNA sequence USA.

Input example

'tsw:opsd_human' is a sequence entry in the example protein database 'tsw'

Database entry: tsw:opsd_human

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   16-JUN-2009, entry version 116.
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., Blocker H.,
RA   Heubner D., Hoerlein A., Michel G., Wedler H., Kohrer K.,
RA   Ottenwalder 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).
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
//

Output file format

The output is a nucleotide sequence containing the most favoured back translation of the specified protein, and using the specified translation table (which defaults to human).

Output example

File: opsd_human.fasta

>OPSD_HUMAN P08100 Rhodopsin (Opsin-2)
ATGAAYGGNACNGARGGNCCNAAYTTYTAYGTNCCNTTYWSNAAYGCNACNGGNGTNGTN
MGNWSNCCNTTYGARTAYCCNCARTAYTAYYTNGCNGARCCNTGGCARTTYWSNATGYTN
GCNGCNTAYATGTTYYTNYTNATHGTNYTNGGNTTYCCNATHAAYTTYYTNACNYTNTAY
GTNACNGTNCARCAYAARAARYTNMGNACNCCNYTNAAYTAYATHYTNYTNAAYYTNGCN
GTNGCNGAYYTNTTYATGGTNYTNGGNGGNTTYACNWSNACNYTNTAYACNWSNYTNCAY
GGNTAYTTYGTNTTYGGNCCNACNGGNTGYAAYYTNGARGGNTTYTTYGCNACNYTNGGN
GGNGARATHGCNYTNTGGWSNYTNGTNGTNYTNGCNATHGARMGNTAYGTNGTNGTNTGY
AARCCNATGWSNAAYTTYMGNTTYGGNGARAAYCAYGCNATHATGGGNGTNGCNTTYACN
TGGGTNATGGCNYTNGCNTGYGCNGCNCCNCCNYTNGCNGGNTGGWSNMGNTAYATHCCN
GARGGNYTNCARTGYWSNTGYGGNATHGAYTAYTAYACNYTNAARCCNGARGTNAAYAAY
GARWSNTTYGTNATHTAYATGTTYGTNGTNCAYTTYACNATHCCNATGATHATHATHTTY
TTYTGYTAYGGNCARYTNGTNTTYACNGTNAARGARGCNGCNGCNCARCARCARGARWSN
GCNACNACNCARAARGCNGARAARGARGTNACNMGNATGGTNATHATHATGGTNATHGCN
TTYYTNATHTGYTGGGTNCCNTAYGCNWSNGTNGCNTTYTAYATHTTYACNCAYCARGGN
WSNAAYTTYGGNCCNATHTTYATGACNATHCCNGCNTTYTTYGCNAARWSNGCNGCNATH
TAYAAYCCNGTNATHTAYATHATGATGAAYAARCARTTYMGNAAYTGYATGYTNACNACN
ATHTGYTGYGGNAARAAYCCNYTNGGNGAYGAYGARGCNWSNGCNACNGTNWSNAARACN
GARACNWSNCARGTNGCNCCNGCN

Data files

The codon usage table is read by default from "Ehum.cut" in the 'data/CODONS' directory of the EMBOSS distribution. If the name of a codon usage file is specified on the command line, then this file will first be searched for in the current directory and then in the 'data/CODONS' directory of the EMBOSS distribution.

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:

.	your current directory
.embossdata/	under your current directory
~/	your home directory
~/.embossdata/	under your home directory

Notes

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.

References

None.

Warnings

None.

Diagnostic Error Messages

"Corrupt codon index file" - the codon usage file is incomplete or empty.

"The file 'drosoph.cut' does not exist" - the codon usage file cannot be opened.

Exit status

This program always exits with a status of 0, unless the codon usage table cannot be opened.

Known bugs

None.

See also

backtranseq	Back-translate a protein sequence to a 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 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)

Author(s)

Alan Bleasby European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK

Please report all bugs to the EMBOSS bug team (emboss-bug (@) emboss.open-bio.org) not to the original author.

History

None

Target users

This program is intended to be used by everyone and everything, from naive users to embedded scripts.

Comments

None