| showorf

## Function

Pretty output of DNA translations

## Description

Showorf displays a nucleic acid sequence with its protein translation in a style suitable for publication. The translation can be done in any frame or combination of frames.

It uses codon frequency files to do the translation. You can specify the codon frequency file that you use with the '-cfile' option. The default table is 'Ehum.cut'.

## Usage

Here is a sample session with showorf

    % showorf
    Pretty output of DNA translations
    Input sequence: tembl:paamir
    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 [paamir.showorf]:

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

## Command line arguments

       Mandatory qualifiers:
      [-sequence]          sequence   Sequence USA
       -frames             menu       Select one or more values
      [-outfile]           outfile    Output file name

       Optional qualifiers:
       -[no]ruler          boolean    Add a ruler
       -[no]plabel         boolean    Number translations
       -[no]nlabel         boolean    Number DNA sequence

       Advanced qualifiers:
       -cfile              codon      Codon usage file
       -width              integer    Width of screen

       Associated qualifiers:
      "-sequence" related qualifiers
       -sbegin1             integer    First base used
       -send1               integer    Last base used, def=seq length
       -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
       -sopenfile1          string     Input filename
       -sdbname1            string     Database name
       -sid1                string     Entryname
       -ufo1                string     UFO features
       -fformat1            string     Features format
       -fopenfile1          string     Features file name
      "-outfile" related qualifiers
       -odirectory2         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 required and optional values
       -debug               boolean    Write debug output to program.dbg
       -acdlog              boolean    Write ACD processing log to program.acdlog
       -acdpretty           boolean    Rewrite ACD file as program.acdpretty
       -acdtable            boolean    Write HTML table of options
       -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 deaths

Mandatory qualifiers | Allowed values | Default
--- | --- | ---
[-sequence] (Parameter 1) | Sequence 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 | <sequence>.showorf
Optional qualifiers | Allowed values | Default
-[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 qualifiers | Allowed values | Default
-cfile | Codon usage file | Codon usage file in EMBOSS data path | Ehum.cut
-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:paamir' is a sequence entry in the example nucleic acid database 'tembl'

### Database entry: tembl:paamir

    ID   PAAMIR     standard; DNA; PRO; 2167 BP.
    XX
    AC   X13776; M43175;
    XX
    SV   X13776.1
    XX
    DT   19-APR-1989 (Rel. 19, Created)
    DT   17-FEB-1997 (Rel. 50, Last updated, Version 22)
    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; gamma subdivision; 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   MEDLINE; 89211409.
    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. 246:39-43(1989).
    XX
    RN   [3]
    RP   1-1292
    RX   MEDLINE; 91317707.
    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. 173:4914-4921(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   SWISS-PROT; P10932; AMIR_PSEAE.
    DR   SWISS-PROT; P27017; AMIC_PSEAE.
    DR   SWISS-PROT; Q51417; AMIS_PSEAE.

      [Part of this file has been deleted for brevity]

    FT                   phenotype"
    FT                   /replace=""
    FT                   /gene="amiC"
    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 Pseudmonas aeruginosa) PAAMIR 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: paamir.showorf

    SHOWORF of PAAMIR 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
--- | ---
backtranseq | Back translate a protein sequence
coderet | Extract CDS, mRNA and translations from feature tables
getorf | Finds and extracts open reading frames (ORFs)
marscan | Finds MAR/SAR sites in nucleic sequences
plotorf | Plot potential open reading frames
prettyseq | Output sequence with translated ranges
remap | Display a sequence with restriction cut sites, translation etc
showseq | Display a sequence with features, translation etc
sixpack | Display a DNA sequence with 6-frame translation and ORFs
syco | Synonymous codon usage Gribskov statistic plot
tcode | Fickett TESTCODE statistic to identify protein-coding DNA
transeq | Translate nucleic acid sequences
wobble | Wobble base plot

## Author(s)

Alan Bleasby (ableasby © hgmp.mrc.ac.uk)
HGMP-RC, Genome Campus, Hinxton, Cambridge CB10 1SB, UK

## History

1999 - written.

## Target users

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

## Comments