| prettyseq

## Wiki

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Please help by correcting and extending the Wiki pages.

## Function

Write a nucleotide sequence and its translation to file

## Description

prettyseq reads a nucleotide sequence and writes an output file containing in a clean format the sequence with the translation (within specified ranges) displayed beneath it. The translated nucleic acid region is given lower-case letters with the rest of the input sequence left in the input case. A specified codon usage table is used to translate the codons.

## Usage

Here is a sample session with prettyseq

    % prettyseq
    Write a nucleotide sequence and its translation to file
    Input nucleotide sequence: tembl:x13776
    Range(s) to translate [1-2167]: 135-1292
    Output file [x13776.prettyseq]:

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

## Command line arguments

    Write a nucleotide sequence and its translation to file
    Version: EMBOSS:6.2.0

       Standard (Mandatory) qualifiers:
      [-sequence]          sequence   Nucleotide sequence filename and optional
                                      format, or reference (input USA)
       -range              range      [Whole sequence] Range(s) to translate
      [-outfile]           outfile    [*.prettyseq] 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    [60] 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 and exit. 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
       -version            boolean    Report version number and exit

Qualifier | Type | Description | Allowed values | Default
--- | --- | --- | --- | ---
Standard (Mandatory) qualifiers
[-sequence] (Parameter 1) | sequence | Nucleotide sequence filename and optional format, or reference (input USA) | Readable sequence | Required
-range | range | Range(s) to translate | Sequence range | Whole sequence
[-outfile] (Parameter 2) | outfile | Output file name | Output file | <*>.prettyseq
Additional (Optional) qualifiers

-table

list

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 | boolean | Add a ruler | Boolean value Yes/No | Yes
-[no]plabel | boolean | Number translations | Boolean value Yes/No | Yes
-[no]nlabel | boolean | Number DNA sequence | Boolean value Yes/No | Yes
Advanced (Unprompted) qualifiers
-width | integer | Width of screen | Integer 10 or more | 60
Associated qualifiers
"-sequence" associated sequence qualifiers
-sbegin1 -sbegin_sequence | integer | Start of the sequence to be used | Any integer value | 0
-send1 -send_sequence | integer | End of the sequence to be used | Any integer value | 0
-sreverse1 -sreverse_sequence | boolean | Reverse (if DNA) | Boolean value Yes/No | N
-sask1 -sask_sequence | boolean | Ask for begin/end/reverse | Boolean value Yes/No | N
-snucleotide1 -snucleotide_sequence | boolean | Sequence is nucleotide | Boolean value Yes/No | N
-sprotein1 -sprotein_sequence | boolean | Sequence is protein | Boolean value Yes/No | N
-slower1 -slower_sequence | boolean | Make lower case | Boolean value Yes/No | N
-supper1 -supper_sequence | boolean | Make upper case | Boolean value Yes/No | N
-sformat1 -sformat_sequence | string | Input sequence format | Any string |
-sdbname1 -sdbname_sequence | string | Database name | Any string |
-sid1 -sid_sequence | string | Entryname | Any string |
-ufo1 -ufo_sequence | string | UFO features | Any string |
-fformat1 -fformat_sequence | string | Features format | Any string |
-fopenfile1 -fopenfile_sequence | string | Features file name | Any string |
"-outfile" associated outfile qualifiers
-odirectory2 -odirectory_outfile | string | Output directory | Any string |
General qualifiers
-auto | boolean | Turn off prompts | Boolean value Yes/No | N
-stdout | boolean | Write first file to standard output | Boolean value Yes/No | N
-filter | boolean | Read first file from standard input, write first file to standard output | Boolean value Yes/No | N
-options | boolean | Prompt for standard and additional values | Boolean value Yes/No | N
-debug | boolean | Write debug output to program.dbg | Boolean value Yes/No | N
-verbose | boolean | Report some/full command line options | Boolean value Yes/No | Y
-help | boolean | Report command line options and exit. More information on associated and general qualifiers can be found with -help -verbose | Boolean value Yes/No | N
-warning | boolean | Report warnings | Boolean value Yes/No | Y
-error | boolean | Report errors | Boolean value Yes/No | Y
-fatal | boolean | Report fatal errors | Boolean value Yes/No | Y
-die | boolean | Report dying program messages | Boolean value Yes/No | Y
-version | boolean | Report version number and exit | Boolean value Yes/No | N

## Input file format

prettyseq reads any 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 (amiR) of
    RT   Pseudomonas 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 sequence 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   InterPro; IPR003211; AmiSUreI_transpt.
    DR   UniProtKB/Swiss-Prot; Q51417; AMIS_PSEAE.

      [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
    //

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

### Output files for usage example

### File: x13776.prettyseq

    PRETTYSEQ of X13776 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

      [Part of this file has been deleted for brevity]

          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.

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

By default, the base and residue numbers of the sequence and its translation are shown beside the sequences in the output. There are options to change this behaviour.

The translation will be shown in a number of sequence regions only. The ranges are specified with the `-range` qualifier. As an alternative to specifying a set of ranges at the command-line, a range file containing such range data may be specified (see "Input File Format").

## 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 | Display the trace in an ABI sequencer file
backtranambig | Back-translate a protein sequence to ambiguous nucleotide sequence
backtranseq | Back-translate a protein sequence to a nucleotide 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 | Draw a helical net for a protein sequence
pepwheel | Draw a helical wheel diagram for a protein sequence
plotorf | Plot potential open reading frames in a nucleotide sequence
prettyplot | Draw a sequence alignment with pretty formatting
remap | Display restriction enzyme binding sites in a nucleotide sequence
seealso | Finds programs with similar function to a specified program
showalign | Display a multiple sequence alignment in pretty format
showdb | Displays information on configured databases
showfeat | Display features of a sequence in pretty format
showorf | Display a nucleotide sequence and translation in pretty format
showpep | Displays protein sequences with features in pretty format
showseq | Displays sequences with features in pretty format
sixpack | Display a DNA sequence with 6-frame translation and ORFs
textsearch | Search the textual description of sequence(s)
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)

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

None