
                             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
