EMBOSS: showorf

| showorf

## Function

Display a nucleotide sequence and translation in pretty format

## Description

showorf writes an input nucleotide sequence and its protein translation to an output file in a clear format that is suitable for publication. The translation can be done in any frame or combination of frames using an (optionally) specified genetic code.

## Usage

Here is a sample session with showorf

    % showorf
    Display a nucleotide sequence and translation in pretty format
    Input nucleotide sequence: tembl:x13776
    Select Frames To Translate
             0 : None
             1 : F1
             2 : F2
             3 : F3
             4 : R1
             5 : R2
             6 : R3
    Select one or more values [1,2,3,4,5,6]:
    Output file [x13776.showorf]:

Go to the input files for this example
Go to the output files for this example

## Command line arguments

       Standard (Mandatory) qualifiers:
      [-sequence]          sequence   Nucleotide sequence filename and optional
                                      format, or reference (input USA)
       -frames             menu       [1,2,3,4,5,6] Select one or more values
                                      (Values: 0 (None); 1 (F1); 2 (F2); 3 (F3); 4
                                      (R1); 5 (R2); 6 (R3))
      [-outfile]           outfile    [*.showorf] Output file name

       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))
       -[no]ruler          boolean    [Y] Add a ruler
       -[no]plabel         boolean    [Y] Number translations
       -[no]nlabel         boolean    [Y] Number DNA sequence

       Advanced (Unprompted) qualifiers:
       -width              integer    [50] Width of screen (Integer 10 or more)

       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
       -odirectory2        string     Output directory

       General qualifiers:
       -auto               boolean    Turn off prompts
       -stdout             boolean    Write first file to standard output
       -filter             boolean    Read first file from standard input, write
                                      first file to 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

Standard (Mandatory) qualifiers | Allowed values | Default
--- | --- | ---
[-sequence] (Parameter 1) | Nucleotide sequence filename and optional format, or reference (input USA) | Readable sequence | Required
-frames | Select one or more values |
0 | (None)
1 | (F1)
2 | (F2)
3 | (F3)
4 | (R1)
5 | (R2)
6 | (R3)
| 1,2,3,4,5,6
[-outfile] (Parameter 2) | Output file name | Output file | <*>.showorf
Additional (Optional) qualifiers | Allowed values | Default
-table | 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
-[no]ruler | Add a ruler | Boolean value Yes/No | Yes
-[no]plabel | Number translations | Boolean value Yes/No | Yes
-[no]nlabel | Number DNA sequence | Boolean value Yes/No | Yes
Advanced (Unprompted) qualifiers | Allowed values | Default
-width | Width of screen | Integer 10 or more | 50

## Input file format

showorf reads a normal nucleic acid sequence USA.

### Input files for usage example

'tembl:x13776' is a sequence entry in the example nucleic acid database 'tembl'

### Database entry: tembl:x13776

    ID   X13776; SV 1; linear; genomic DNA; STD; PRO; 2167 BP.
    XX
    AC   X13776; M43175;
    XX
    DT   19-APR-1989 (Rel. 19, Created)
    DT   14-NOV-2006 (Rel. 89, Last updated, Version 24)
    XX
    DE   Pseudomonas aeruginosa amiC and amiR gene for aliphatic amidase regulation
    XX
    KW   aliphatic amidase regulator; amiC gene; amiR gene.
    XX
    OS   Pseudomonas aeruginosa
    OC   Bacteria; Proteobacteria; Gammaproteobacteria; Pseudomonadales;
    OC   Pseudomonadaceae; Pseudomonas.
    XX
    RN   [1]
    RP   1167-2167
    RA   Rice P.M.;
    RT   ;
    RL   Submitted (16-DEC-1988) to the EMBL/GenBank/DDBJ databases.
    RL   Rice P.M., EMBL, Postfach 10-2209, Meyerhofstrasse 1, 6900 Heidelberg, FRG.
    XX
    RN   [2]
    RP   1167-2167
    RX   DOI; 10.1016/0014-5793(89)80249-2.
    RX   PUBMED; 2495988.
    RA   Lowe N., Rice P.M., Drew R.E.;
    RT   "Nucleotide sequence of the aliphatic amidase regulator gene of Pseudomonas
    RT   aeruginosa";
    RL   FEBS Lett. 246(1-2):39-43(1989).
    XX
    RN   [3]
    RP   1-1292
    RX   PUBMED; 1907262.
    RA   Wilson S., Drew R.;
    RT   "Cloning and DNA seqence of amiC, a new gene regulating expression of the
    RT   Pseudomonas aeruginosa aliphatic amidase, and purification of the amiC
    RT   product.";
    RL   J. Bacteriol. 173(16):4914-4921(1991).
    XX
    RN   [4]
    RP   1-2167
    RA   Rice P.M.;
    RT   ;
    RL   Submitted (04-SEP-1991) to the EMBL/GenBank/DDBJ databases.
    RL   Rice P.M., EMBL, Postfach 10-2209, Meyerhofstrasse 1, 6900 Heidelberg, FRG.
    XX
    DR   GOA; Q51417.
    DR   UniProtKB/Swiss-Prot; Q51417; AMIS_PSEAE.
    XX

      [Part of this file has been deleted for brevity]

    FT                   /replace=""
    FT                   /note="ClaI fragment deleted in pSW36,  constitutive
    FT                   phenotype"
    FT   misc_feature    1
    FT                   /note="last base of an XhoI site"
    FT   misc_feature    648..653
    FT                   /note="end of 658bp XhoI fragment, deletion in  pSW3 causes
    FT                   constitutive expression of amiE"
    FT   conflict        1281
    FT                   /replace="g"
    FT                   /citation=[3]
    XX
    SQ   Sequence 2167 BP; 363 A; 712 C; 730 G; 362 T; 0 other;
         ggtaccgctg gccgagcatc tgctcgatca ccaccagccg ggcgacggga actgcacgat        60
         ctacctggcg agcctggagc acgagcgggt tcgcttcgta cggcgctgag cgacagtcac       120
         aggagaggaa acggatggga tcgcaccagg agcggccgct gatcggcctg ctgttctccg       180
         aaaccggcgt caccgccgat atcgagcgct cgcacgcgta tggcgcattg ctcgcggtcg       240
         agcaactgaa ccgcgagggc ggcgtcggcg gtcgcccgat cgaaacgctg tcccaggacc       300
         ccggcggcga cccggaccgc tatcggctgt gcgccgagga cttcattcgc aaccgggggg       360
         tacggttcct cgtgggctgc tacatgtcgc acacgcgcaa ggcggtgatg ccggtggtcg       420
         agcgcgccga cgcgctgctc tgctacccga ccccctacga gggcttcgag tattcgccga       480
         acatcgtcta cggcggtccg gcgccgaacc agaacagtgc gccgctggcg gcgtacctga       540
         ttcgccacta cggcgagcgg gtggtgttca tcggctcgga ctacatctat ccgcgggaaa       600
         gcaaccatgt gatgcgccac ctgtatcgcc agcacggcgg cacggtgctc gaggaaatct       660
         acattccgct gtatccctcc gacgacgact tgcagcgcgc cgtcgagcgc atctaccagg       720
         cgcgcgccga cgtggtcttc tccaccgtgg tgggcaccgg caccgccgag ctgtatcgcg       780
         ccatcgcccg tcgctacggc gacggcaggc ggccgccgat cgccagcctg accaccagcg       840
         aggcggaggt ggcgaagatg gagagtgacg tggcagaggg gcaggtggtg gtcgcgcctt       900
         acttctccag catcgatacg cccgccagcc gggccttcgt ccaggcctgc catggtttct       960
         tcccggagaa cgcgaccatc accgcctggg ccgaggcggc ctactggcag accttgttgc      1020
         tcggccgcgc cgcgcaggcc gcaggcaact ggcgggtgga agacgtgcag cggcacctgt      1080
         acgacatcga catcgacgcg ccacaggggc cggtccgggt ggagcgccag aacaaccaca      1140
         gccgcctgtc ttcgcgcatc gcggaaatcg atgcgcgcgg cgtgttccag gtccgctggc      1200
         agtcgcccga accgattcgc cccgaccctt atgtcgtcgt gcataacctc gacgactggt      1260
         ccgccagcat gggcggggga ccgctcccat gagcgccaac tcgctgctcg gcagcctgcg      1320
         cgagttgcag gtgctggtcc tcaacccgcc gggggaggtc agcgacgccc tggtcttgca      1380
         gctgatccgc atcggttgtt cggtgcgcca gtgctggccg ccgccggaag ccttcgacgt      1440
         gccggtggac gtggtcttca ccagcatttt ccagaatggc caccacgacg agatcgctgc      1500
         gctgctcgcc gccgggactc cgcgcactac cctggtggcg ctggtggagt acgaaagccc      1560
         cgcggtgctc tcgcagatca tcgagctgga gtgccacggc gtgatcaccc agccgctcga      1620
         tgcccaccgg gtgctgcctg tgctggtatc ggcgcggcgc atcagcgagg aaatggcgaa      1680
         gctgaagcag aagaccgagc agctccagga ccgcatcgcc ggccaggccc ggatcaacca      1740
         ggccaaggtg ttgctgatgc agcgccatgg ctgggacgag cgcgaggcgc accagcacct      1800
         gtcgcgggaa gcgatgaagc ggcgcgagcc gatcctgaag atcgctcagg agttgctggg      1860
         aaacgagccg tccgcctgag cgatccgggc cgaccagaac aataacaaga ggggtatcgt      1920
         catcatgctg ggactggttc tgctgtacgt tggcgcggtg ctgtttctca atgccgtctg      1980
         gttgctgggc aagatcagcg gtcgggaggt ggcggtgatc aacttcctgg tcggcgtgct      2040
         gagcgcctgc gtcgcgttct acctgatctt ttccgcagca gccgggcagg gctcgctgaa      2100
         ggccggagcg ctgaccctgc tattcgcttt tacctatctg tgggtggccg ccaaccagtt      2160
         cctcgag                                                                2167
    //

## Output file format

As a sequence with high GC content (from Pseudomonas aeruginosa) X13776 has several overlapping open reading frames.

The true ORFs are 1..109 (amiB partial) 135..1292 (amiC) 1289..1879 (amiR) 1925..end (amiS partial)

### Output files for usage example

### File: x13776.showorf

    SHOWORF of X13776 from 1 to 2167

               ---------|---------|---------|---------|---------|
             1 ggtaccgctggccgagcatctgctcgatcaccaccagccgggcgacggga 50
    F1       1 G  T  A  G  R  A  S  A  R  S  P  P  A  G  R  R  E  17
    F2       1  V  P  L  A  E  H  L  L  D  H  H  Q  P  G  D  G  N 17
    F3       1   Y  R  W  P  S  I  C  S  I  T  T  S  R  A  T  G   16
    R1       9   T  G  S  A  S  C  R  S  S  *  W  W  G  P  S  P   5
    R2     106    Y  R  Q  G  L  M  Q  E  I  V  V  L  R  A  V  P  91
    R3      38     V  A  P  R  A  D  A  R  D  G  G  A  P  R  R  S 23

               ---------|---------|---------|---------|---------|
            51 actgcacgatctacctggcgagcctggagcacgagcgggttcgcttcgta 100
    F1      18  L  H  D  L  P  G  E  P  G  A  R  A  G  S  L  R  T 34
    F2      18   C  T  I  Y  L  A  S  L  E  H  E  R  V  R  F  V   33
    F3      17 T  A  R  S  T  W  R  A  W  S  T  S  G  F  A  S  Y  33
    R1       4 F  Q  V  I  *  R  A  L  R  S  C  S  R  T  R  K  T  31
    R2      90  V  A  R  D  V  Q  R  A  Q  L  V  L  P  N  A  E  Y 74
    R3      22   S  C  S  R  G  P  S  G  P  A  R  A  P  E  S  R   7

               ---------|---------|---------|---------|---------|
           101 cggcgctgagcgacagtcacaggagaggaaacggatgggatcgcaccagg 150
    F1      35   A  L  S  D  S  H  R  R  G  N  G  W  D  R  T  R   50
    F2      34 R  R  *  A  T  V  T  G  E  E  T  D  G  I  A  P  G  14
    F3      34  G  A  E  R  Q  S  Q  E  R  K  R  M  G  S  H  Q  E 50
    R1      30  R  R  Q  A  V  T  V  P  S  S  V  S  P  I  A  G  P 14
    R2      73   P  A  S  R  C  D  C  S  L  F  R  I  P  D  C  W   58
    R3       6 V  A  S  L  S  L  *  L  L  P  F  P  H  S  R  V  L  398

               ---------|---------|---------|---------|---------|
           151 agcggccgctgatcggcctgctgttctccgaaaccggcgtcaccgccgat 200
    F1      51 S  G  R  *  S  A  C  C  S  P  K  P  A  S  P  P  I  13
    F2      15  A  A  A  D  R  P  A  V  L  R  N  R  R  H  R  R  Y 31
    F3      51   R  P  L  I  G  L  L  F  S  E  T  G  V  T  A  D   66
    R1      13   A  A  A  S  R  G  A  T  R  R  F  R  R  *  R  R   49
    R2      57 S  R  G  S  I  P  R  S  N  E  S  V  P  T  V  A  S  41
    R3     397  L  P  R  Q  D  A  Q  Q  E  G  F  G  A  D  G  G  I 381

               ---------|---------|---------|---------|---------|
           201 atcgagcgctcgcacgcgtatggcgcattgctcgcggtcgagcaactgaa 250
    F1      14  S  S  A  R  T  R  M  A  H  C  S  R  S  S  N  *  T 1
    F2      32   R  A  L  A  R  V  W  R  I  A  R  G  R  A  T  E   47
    F3      67 I  E  R  S  H  A  Y  G  A  L  L  A  V  E  Q  L  N  83
    R1      48 Y  R  A  S  A  R  T  H  R  M  A  R  P  R  A  V  S  32
    R2      40  I  S  R  E  C  A  Y  P  A  N  S  A  T  S  C  S  F 24
    R3     380   D  L  A  R  V  R  I  A  C  Q  E  R  D  L  L  Q   365

               ---------|---------|---------|---------|---------|
           251 ccgcgagggcggcgtcggcggtcgcccgatcgaaacgctgtcccaggacc 300
    F1       2   A  R  A  A  S  A  V  A  R  S  K  R  C  P  R  T   17

      [Part of this file has been deleted for brevity]

    F2       8 N  N  K  R  G  I  V  I  M  L  G  L  V  L  L  Y  V  24
    F3      22  I  T  R  G  V  S  S  S  C  W  D  W  F  C  C  T  L 38
    R1      53  L  L  L  L  P  I  T  M  M  S  P  S  T  R  S  Y  T 37
    R2      73   I  V  L  P  T  D  D  D  H  Q  S  Q  N  Q  Q  V   58
    R3       7 C  Y  C  S  P  Y  R  *  *  A  P  V  P  E  A  T  R  7

               ---------|---------|---------|---------|---------|
          1951 tggcgcggtgctgtttctcaatgccgtctggttgctgggcaagatcagcg 2000
    F1      16 W  R  G  A  V  S  Q  C  R  L  V  A  G  Q  D  Q  R  32
    F2      25  G  A  V  L  F  L  N  A  V  W  L  L  G  K  I  S  G 41
    F3      39   A  R  C  C  F  S  M  P  S  G  C  W  A  R  S  A   54
    R1      36   P  A  T  S  N  R  L  A  T  Q  N  S  P  L  I  L   21
    R2      57 N  A  R  H  Q  K  E  I  G  D  P  Q  Q  A  L  D  A  41
    R3       6  Q  R  P  A  T  E  *  H  R  R  T  A  P  C  S  *  R 7

               ---------|---------|---------|---------|---------|
          2001 gtcgggaggtggcggtgatcaacttcctggtcggcgtgctgagcgcctgc 2050
    F1      33  S  G  G  G  G  D  Q  L  P  G  R  R  A  E  R  L  R 49
    F2      42   R  E  V  A  V  I  N  F  L  V  G  V  L  S  A  C   57
    F3      55 V  G  R  W  R  *  S  T  S  W  S  A  C  *  A  P  A  3
    R1      20 P  R  S  T  A  T  I  L  K  R  T  P  T  S  L  A  Q  4
    R2      40  T  P  L  H  R  H  D  V  E  Q  D  A  H  Q  A  G  A 24
    R3       6   D  P  P  P  P  S  *  S  G  P  R  R  A  S  R  R   28

               ---------|---------|---------|---------|---------|
          2051 gtcgcgttctacctgatcttttccgcagcagccgggcagggctcgctgaa 2100
    F1      50   R  V  L  P  D  L  F  R  S  S  R  A  G  L  A  E   65
    F2      58 V  A  F  Y  L  I  F  S  A  A  A  G  Q  G  S  L  K  74
    F3       4  S  R  S  T  *  S  F  P  Q  Q  P  G  R  A  R  *  R 1
    R1       3  T  A  N  *  R  I  K  E  A  A  A  P  C  P  E  S  F 12
    R2      23   D  R  E  V  Q  D  K  G  C  C  G  P  L  A  R  Q   8
    R3      27 R  R  T  R  G  S  R  K  R  L  L  R  A  P  S  A  S  11

               ---------|---------|---------|---------|---------|
          2101 ggccggagcgctgaccctgctattcgcttttacctatctgtgggtggccg 2150
    F1      66 G  R  S  A  D  P  A  I  R  F  Y  L  S  V  G  G  R  82
    F2      75  A  G  A  L  T  L  L  F  A  F  T  Y  L  W  V  A  A 91
    F3       2   P  E  R  *  P  C  Y  S  L  L  P  I  C  G  W  P   12
    R1      11   A  P  A  S  V  R  S  N  A  K  V  *  R  H  T  A   7
    R2       7 L  G  S  R  Q  G  Q  *  E  S  K  G  I  Q  P  H  G  7
    R3      10  P  R  L  A  S  G  A  I  R  K  *  R  D  T  P  P  R 6

               ---------|-------
          2151 ccaaccagttcctcgag 2167
    F1      83  Q  P  V  P  R    87
    F2      92   N  Q  F  L  E   96
    F3      13 P  T  S  S  S     17
    R1       6 A  L  W  N  R  S  1
    R2       6  G  V  L  E  E  L 1
    R3       5   W  G  T  G  R   1

## Data files

Showorf uses the codon frequency files to translate the sequence.

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 with the '-cfile' option, then this file will first be searched for in the current directory and then in the 'data/CODONS' directory of the EMBOSS distribution.

To see the available EMBOSS codon usage files, run:

    % embossdata -showall

To fetch one of the codon usage tables (for example 'Emus.cut') into your current directory for you to inspect or modify, run:

    % embossdata -fetch -file Emus.cut

## Notes

None.

## References

None.

## Warnings

None.

## Diagnostic Error Messages

None.

## Exit status

It exits with a status of 0. It always exits with status 0.

## Known bugs

None.

## See also

Program name | Description
--- | ---
backtranambig | Back-translate a protein sequence to ambiguous nucleotide sequence
backtranseq | Back-translate a protein sequence to a nucleotide sequence
coderet | Extract CDS, mRNA and translations from feature tables
getorf | Finds and extracts open reading frames (ORFs)
marscan | Finds matrix/scaffold recognition (MRS) signatures in DNA sequences
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
showseq | Displays sequences with features in pretty format
sixpack | Display a DNA sequence with 6-frame translation and ORFs
syco | Draw synonymous codon usage statictic plot for a nucleotide sequence
tcode | Identify protein-coding regions using Fickett TESTCODE statistic
transeq | Translate nucleic acid sequences
wobble | Plot third base position variability in a nucleotide sequence

## Author(s)

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

## History

1999 - written - Alan Bleasby

## Target users

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

## Comments

None