EMBOSS: showorf

| ## EMBOSS: showorf

# Program 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: embl: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]:

## 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          bool       Add a ruler
       -[no]plabel         bool       Number translations
       -[no]nlabel         bool       Number DNA sequence

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

       General qualifiers:
      -help                bool       report command line options. More
                                      information on associated and general
                                      qualifiers can be found with -help -verbose

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 | Yes/No | Yes
-[no]plabel | Number translations | Yes/No | Yes
-[no]nlabel | Number DNA sequence | 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

Nucleic acid sequence USA

## Output file format

Here is some of the output from the example run. 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)

    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

               ---------|---------|---------|---------|---------|
            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

               ---------|---------|---------|---------|---------|
           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

    ......................

               ---------|---------|---------|---------|---------|
          1851 agttgctgggaaacgagccgtccgcctgagcgatccgggccgaccagaac 1900
    F1     341  V  A  G  K  R  A  V  R  L  S  D  P  G  R  P  E  Q 357
    F2     203   L  L  G  N  E  P  S  A  *  A  I  R  A  D  Q  N   7
    F3       5 S  C  W  E  T  S  R  P  P  E  R  S  G  P  T  R  T  21

               ---------|---------|---------|---------|---------|
          1901 aataacaagaggggtatcgtcatcatgctgggactggttctgctgtacgt 1950
    F1       1   *  Q  E  G  Y  R  H  H  A  G  T  G  S  A  V  R   15
    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

               ---------|---------|---------|---------|---------|
          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

               ---------|---------|---------|---------|---------|
          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

               ---------|---------|---------|---------|---------|
          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

               ---------|---------|---------|---------|---------|
          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

               ---------|-------
          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

## 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

## References

## Warnings

## Diagnostic Error Messages

## Exit status

It always exits with status 0.

## Known bugs

## 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
transeq | Translate nucleic acid sequences
wobble | Wobble base plot

## Author(s)

This application was written by Alan Bleasby (ableasby@hgmp.mrc.ac.uk)

## History

## Target users

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

## Comments