EMBOSS: prettyseq

| ## EMBOSS: prettyseq

# Program prettyseq

## Function

Output sequence with translated ranges

## Description

This writes out a nicely formatted display of the sequence with the translation (within specified ranges) displayed beneath it.

The translated nucleic acid region will be shown in lower-case letters while the rest of the input sequence will be left in the input case.

The base and residue numbers of the sequences are shown beside the sequences in the output.

Slightly unusually, this application uses the codon usage tables to translate the codons.

## Usage

Here is a sample session with prettyseq.

    % prettyseq
    Output sequence with translated ranges
    Input sequence: embl:paamir
    Range(s) to translate [1-2167]: 135-1292
    Output file [paamir.prettyseq]:

## Command line arguments

       Mandatory qualifiers:
      [-sequence]          sequence   Sequence USA
       -range              range      Range(s) to translate
      [-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
-range | Range(s) to translate | Sequence range | Whole sequence
[-outfile] (Parameter 2) | Output file name | Output file | <sequence>.prettyseq
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 | 60

## Input file format

You can specifiy a file of ranges to extract by giving the '-range' qualifier the value '@' followed by the name of the file containing the ranges. (eg: '-range @myfile').

The format of the range file is:

- Comment lines start with '#' in the first column.
- Comment lines and blank lines are ignored.
- The line may start with white-space.
- There are two positive (integer) numbers per line separated by one or more space or TAB characters.
- The second number must be greater or equal to the first number.
- There can be optional text after the two numbers to annotate the line.
- White-space before or after the text is removed.

An example range file is:

    # this is my set of ranges
    12   23
     4   5       this is like 12-23, but smaller
    67   10348   interesting region

## Output file format

Here is the output from the example run.

    PRETTYSEQ of PAAMIR from 1 to 2167

               ---------|---------|---------|---------|---------|---------|
             1 GGTACCGCTGGCCGAGCATCTGCTCGATCACCACCAGCCGGGCGACGGGAACTGCACGAT 60

               ---------|---------|---------|---------|---------|---------|
            61 CTACCTGGCGAGCCTGGAGCACGAGCGGGTTCGCTTCGTACGGCGCTGAGCGACAGTCAC 120

               ---------|---------|---------|---------|---------|---------|
           121 AGGAGAGGAAACGGatgggatcgcaccaggagcggccgctgatcggcctgctgttctccg 180
             1               M  G  S  H  Q  E  R  P  L  I  G  L  L  F  S  E 16

               ---------|---------|---------|---------|---------|---------|
           181 aaaccggcgtcaccgccgatatcgagcgctcgcacgcgtatggcgcattgctcgcggtcg 240
            17   T  G  V  T  A  D  I  E  R  S  H  A  Y  G  A  L  L  A  V  E 36

               ---------|---------|---------|---------|---------|---------|
           241 agcaactgaaccgcgagggcggcgtcggcggtcgcccgatcgaaacgctgtcccaggacc 300
            37   Q  L  N  R  E  G  G  V  G  G  R  P  I  E  T  L  S  Q  D  P 56

               ---------|---------|---------|---------|---------|---------|
           301 ccggcggcgacccggaccgctatcggctgtgcgccgaggacttcattcgcaaccgggggg 360
            57   G  G  D  P  D  R  Y  R  L  C  A  E  D  F  I  R  N  R  G  V 76

               ---------|---------|---------|---------|---------|---------|
           361 tacggttcctcgtgggctgctacatgtcgcacacgcgcaaggcggtgatgccggtggtcg 420
            77   R  F  L  V  G  C  Y  M  S  H  T  R  K  A  V  M  P  V  V  E 96

               ---------|---------|---------|---------|---------|---------|
           421 agcgcgccgacgcgctgctctgctacccgaccccctacgagggcttcgagtattcgccga 480
            97   R  A  D  A  L  L  C  Y  P  T  P  Y  E  G  F  E  Y  S  P  N 116

               ---------|---------|---------|---------|---------|---------|
           481 acatcgtctacggcggtccggcgccgaaccagaacagtgcgccgctggcggcgtacctga 540
           117   I  V  Y  G  G  P  A  P  N  Q  N  S  A  P  L  A  A  Y  L  I 136

               ---------|---------|---------|---------|---------|---------|
           541 ttcgccactacggcgagcgggtggtgttcatcggctcggactacatctatccgcgggaaa 600
           137   R  H  Y  G  E  R  V  V  F  I  G  S  D  Y  I  Y  P  R  E  S 156

               ---------|---------|---------|---------|---------|---------|
           601 gcaaccatgtgatgcgccacctgtatcgccagcacggcggcacggtgctcgaggaaatct 660
           157   N  H  V  M  R  H  L  Y  R  Q  H  G  G  T  V  L  E  E  I  Y 176

               ---------|---------|---------|---------|---------|---------|
           661 acattccgctgtatccctccgacgacgacttgcagcgcgccgtcgagcgcatctaccagg 720
           177   I  P  L  Y  P  S  D  D  D  L  Q  R  A  V  E  R  I  Y  Q  A 196

               ---------|---------|---------|---------|---------|---------|
           721 cgcgcgccgacgtggtcttctccaccgtggtgggcaccggcaccgccgagctgtatcgcg 780
           197   R  A  D  V  V  F  S  T  V  V  G  T  G  T  A  E  L  Y  R  A 216

               ---------|---------|---------|---------|---------|---------|
           781 ccatcgcccgtcgctacggcgacggcaggcggccgccgatcgccagcctgaccaccagcg 840
           217   I  A  R  R  Y  G  D  G  R  R  P  P  I  A  S  L  T  T  S  E 236

               ---------|---------|---------|---------|---------|---------|
           841 aggcggaggtggcgaagatggagagtgacgtggcagaggggcaggtggtggtcgcgcctt 900
           237   A  E  V  A  K  M  E  S  D  V  A  E  G  Q  V  V  V  A  P  Y 256

               ---------|---------|---------|---------|---------|---------|
           901 acttctccagcatcgatacgcccgccagccgggccttcgtccaggcctgccatggtttct 960
           257   F  S  S  I  D  T  P  A  S  R  A  F  V  Q  A  C  H  G  F  F 276

               ---------|---------|---------|---------|---------|---------|
           961 tcccggagaacgcgaccatcaccgcctgggccgaggcggcctactggcagaccttgttgc 1020
           277   P  E  N  A  T  I  T  A  W  A  E  A  A  Y  W  Q  T  L  L  L 296

               ---------|---------|---------|---------|---------|---------|
          1021 tcggccgcgccgcgcaggccgcaggcaactggcgggtggaagacgtgcagcggcacctgt 1080
           297   G  R  A  A  Q  A  A  G  N  W  R  V  E  D  V  Q  R  H  L  Y 316

               ---------|---------|---------|---------|---------|---------|
          1081 acgacatcgacatcgacgcgccacaggggccggtccgggtggagcgccagaacaaccaca 1140
           317   D  I  D  I  D  A  P  Q  G  P  V  R  V  E  R  Q  N  N  H  S 336

               ---------|---------|---------|---------|---------|---------|
          1141 gccgcctgtcttcgcgcatcgcggaaatcgatgcgcgcggcgtgttccaggtccgctggc 1200
           337   R  L  S  S  R  I  A  E  I  D  A  R  G  V  F  Q  V  R  W  Q 356

               ---------|---------|---------|---------|---------|---------|
          1201 agtcgcccgaaccgattcgccccgacccttatgtcgtcgtgcataacctcgacgactggt 1260
           357   S  P  E  P  I  R  P  D  P  Y  V  V  V  H  N  L  D  D  W  S 376

               ---------|---------|---------|---------|---------|---------|
          1261 ccgccagcatgggcgggggaccgctcccatgaGCGCCAACTCGCTGCTCGGCAGCCTGCG 1320
           377   A  S  M  G  G  G  P  L  P  *                               385

               ---------|---------|---------|---------|---------|---------|
          1321 CGAGTTGCAGGTGCTGGTCCTCAACCCGCCGGGGGAGGTCAGCGACGCCCTGGTCTTGCA 1380

               ---------|---------|---------|---------|---------|---------|
          1381 GCTGATCCGCATCGGTTGTTCGGTGCGCCAGTGCTGGCCGCCGCCGGAAGCCTTCGACGT 1440

               ---------|---------|---------|---------|---------|---------|
          1441 GCCGGTGGACGTGGTCTTCACCAGCATTTTCCAGAATGGCCACCACGACGAGATCGCTGC 1500

               ---------|---------|---------|---------|---------|---------|
          1501 GCTGCTCGCCGCCGGGACTCCGCGCACTACCCTGGTGGCGCTGGTGGAGTACGAAAGCCC 1560

               ---------|---------|---------|---------|---------|---------|
          1561 CGCGGTGCTCTCGCAGATCATCGAGCTGGAGTGCCACGGCGTGATCACCCAGCCGCTCGA 1620

               ---------|---------|---------|---------|---------|---------|
          1621 TGCCCACCGGGTGCTGCCTGTGCTGGTATCGGCGCGGCGCATCAGCGAGGAAATGGCGAA 1680

               ---------|---------|---------|---------|---------|---------|
          1681 GCTGAAGCAGAAGACCGAGCAGCTCCAGGACCGCATCGCCGGCCAGGCCCGGATCAACCA 1740

               ---------|---------|---------|---------|---------|---------|
          1741 GGCCAAGGTGTTGCTGATGCAGCGCCATGGCTGGGACGAGCGCGAGGCGCACCAGCACCT 1800

               ---------|---------|---------|---------|---------|---------|
          1801 GTCGCGGGAAGCGATGAAGCGGCGCGAGCCGATCCTGAAGATCGCTCAGGAGTTGCTGGG 1860

               ---------|---------|---------|---------|---------|---------|
          1861 AAACGAGCCGTCCGCCTGAGCGATCCGGGCCGACCAGAACAATAACAAGAGGGGTATCGT 1920

               ---------|---------|---------|---------|---------|---------|
          1921 CATCATGCTGGGACTGGTTCTGCTGTACGTTGGCGCGGTGCTGTTTCTCAATGCCGTCTG 1980

               ---------|---------|---------|---------|---------|---------|
          1981 GTTGCTGGGCAAGATCAGCGGTCGGGAGGTGGCGGTGATCAACTTCCTGGTCGGCGTGCT 2040

               ---------|---------|---------|---------|---------|---------|
          2041 GAGCGCCTGCGTCGCGTTCTACCTGATCTTTTCCGCAGCAGCCGGGCAGGGCTCGCTGAA 2100

               ---------|---------|---------|---------|---------|---------|
          2101 GGCCGGAGCGCTGACCCTGCTATTCGCTTTTACCTATCTGTGGGTGGCCGCCAACCAGTT 2160

               -------
          2161 CCTCGAG 2167

## 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.

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

"Range outside length of sequence" - this is self explanatory. You should specify a range of sequences to translate that is within the length of the input sequence.

## Exit status

It always exits with a status of 0.

## Known bugs

None.

## See also

Program name | Description
--- | ---
abiview | Reads ABI file and display the trace
backtranseq | Back translate a protein sequence
cirdna | Draws circular maps of DNA constructs
coderet | Extract CDS, mRNA and translations from feature tables
lindna | Draws linear maps of DNA constructs
pepnet | Displays proteins as a helical net
pepwheel | Shows protein sequences as helices
plotorf | Plot potential open reading frames
prettyplot | Displays aligned sequences, with colouring and boxing
remap | Display a sequence with restriction cut sites, translation etc
seealso | Finds programs sharing group names
showalign | Displays a multiple sequence alignment
showdb | Displays information on the currently available databases
showfeat | Show features of a sequence
showorf | Pretty output of DNA translations
showseq | Display a sequence with features, translation etc
textsearch | Search sequence documentation text. SRS and Entrez are faster!
transeq | Translate nucleic acid sequences

showseq has more options for specifying various ways of displaying a sequence, with or without various ways of translating it.

## Author(s)

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

## History

Written (1999) - Alan Bleasby

## Target users

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

## Comments