
                               backtranambig 



Function

   Back translate a protein sequence to ambiguous codons

Description

   backtranambig takes a protein sequence and makes the nucleic acid
   sequence it could have come from. It does this by generating
   nucleotide ambiguity codes that represent all possible codons for each
   amino acid.

   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.

  Genetic code

   backtranambig needs a genetic code to generate the ambiguous codons.
   The default genetic code is the standard ('Universal') code.

Usage

   Here is a sample session with 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

Command line arguments

   Standard (Mandatory) qualifiers:
  [-sequence]          sequence   (Gapped) protein sequence filename and
                                  optional format, or reference (input USA)
  [-outfile]           seqout     [.] (Gapped) nucleotide
                                  sequence filename and optional format
                                  (output USA)

   Additional (Optional) qualifiers:
   -table              menu       [0] Genetic code to use (Values: 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))

   Advanced (Unprompted) qualifiers: (none)
   Associated qualifiers:

   "-sequence" associated qualifiers
   -sbegin1            integer    Start of the sequence to be used
   -send1              integer    End of the sequence to be used
   -sreverse1          boolean    Reverse (if DNA)
   -sask1              boolean    Ask for begin/end/reverse
   -snucleotide1       boolean    Sequence is nucleotide
   -sprotein1          boolean    Sequence is protein
   -slower1            boolean    Make lower case
   -supper1            boolean    Make upper case
   -sformat1           string     Input sequence format
   -sdbname1           string     Database name
   -sid1               string     Entryname
   -ufo1               string     UFO features
   -fformat1           string     Features format
   -fopenfile1         string     Features file name

   "-outfile" associated qualifiers
   -osformat2          string     Output seq format
   -osextension2       string     File name extension
   -osname2            string     Base file name
   -osdirectory2       string     Output directory
   -osdbname2          string     Database name to add
   -ossingle2          boolean    Separate file for each entry
   -oufo2              string     UFO features
   -offormat2          string     Features format
   -ofname2            string     Features file name
   -ofdirectory2       string     Output directory

   General qualifiers:
   -auto               boolean    Turn off prompts
   -stdout             boolean    Write standard output
   -filter             boolean    Read standard input, write standard output
   -options            boolean    Prompt for standard and additional values
   -debug              boolean    Write debug output to program.dbg
   -verbose            boolean    Report some/full command line options
   -help               boolean    Report command line options. More
                                  information on associated and general
                                  qualifiers can be found with -help -verbose
   -warning            boolean    Report warnings
   -error              boolean    Report errors
   -fatal              boolean    Report fatal errors
   -die                boolean    Report dying program messages

Input file format

   Any DNA sequence USA.

  Input files for usage 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   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
//

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 files for usage 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

Notes

   None.

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

   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

Author(s)

   Alan Bleasby (ajb © ebi.ac.uk)
   European Bioinformatics Institute, Wellcome Trust Genome Campus,
   Hinxton, Cambridge CB10 1SD, UK

History

   None

Target users

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

Comments

   None
