Mytrans

• MYTRANS
  • FUNCTION
  • DESCRIPTION
  • AUTHOR
  • EXAMPLE
  • OUTPUT
  • INPUT FILE
  • RELATED PROGRAMS
  • COMMAND-LINE SUMMARY
  • LOCAL DATA FILES

MYTRANS

FUNCTION

MyTrans is a simple EGCG application that translates part of a nucleotide sequence into protein.

DESCRIPTION

MyTrans is a simple application which reads in a nucleotide sequence, prompts for a sequence range, and reports the translation.

The program is very short, and can be used as a model for users to build their own sequence analysis applications.

AUTHOR

This program was written by Peter Rice (E-mail: pmr@sanger.ac.uk Post: Informatics Division, The Sanger Centre, Hinxton Hall, Cambridge, CB10 1RQ, UK).

All EGCG programs are supported by the EGCG Support Team, who can be contacted by E-mail (egcg@embnet.org).

EXAMPLE

Here is a sample session with MyTrans

  
  
  % mytrans
  
   MYTRANS uses nucleotide sequence data
  
   MYTRANS of what sequence ?  GenEmbl:paamir
  
                Start (* 1 *) ?  1289
                End (* 2167 *) ?  1879
            Reverse (* No *) ?
  
   What should I call the output file (* paamir.trans *) ?
  
  %
  

OUTPUT

The output from MyTrans is a protein sequence in GCG format.

  
  
  MYTRANS of em_ba:paamir check 3726 from 1289 to 1879
  paamir.trans  Length: 197  September 21, 1995 13:19  Type: P  Check: 2253  ..
  
    1  MSANSLLGSL RELQVLVLNP PGEVSDALVL QLIRIGCSVR QCWPPPEAFD
  
   51  VPVDVVFTSI FQNGHHDEIA ALLAAGTPRT TLVALVEYES PAVLSQIIEL
  
  101  ECHGVITQPL DAHRVLPVLV SARRISEEMA KLKQKTEQLQ DRIAGQARIN
  
  151  QAKVLLMQRH GWDEREAHQH LSREAMKRRE PILKIAQELL GNEPSA*
  
  

INPUT FILE

The input file for MyTrans is a GCG nucleotide sequence file.

RELATED PROGRAMS

ETranslate is a version of GCG's old Translate program with command line control added. EExtractPeptide is a version of ExtractPeptide with command line control. ExtractPeptide writes a peptide sequence from one or more of the translation frames displayed in the output from Map. Translate supercedes ExtractPeptide for most applications. AllTrans translates a set of aligned nucleotide sequences into protein.

COMMAND-LINE SUMMARY

All parameters for this program may be put on the command line. Use the option -CHEck to see the summary below and to have a chance to add things to the command line before the program executes. In the summary below, the capitalized letters in the qualifier names are the letters that you must type in order to use the parameter. Square brackets ([ and ]) enclose qualifiers or parameter values that are optional. For more information, see "Using Program Parameters" in Chapter 3, Basic Concepts: Using Programs in the GCG User's Guide.

  
  
  Minimum syntax: % mytrans [-INfile=]GenEmbl:paamir -Default
  
  Prompted Parameters:
  
  -BEGin=1 -END=2167          Range of interest
  -REVerse=1                  Sequence direction
  [-OUTfile=]paamir.trans     Output file
  
  Local Data Files:
  
  -DATa=translate.txt         Translation table
  
  Optional Parameters: None
  

LOCAL DATA FILES

The files described below supply auxiliary data to this program. The program automatically reads them from a public data directory unless you either 1) have a data file with exactly the same name in your current working directory; or 2) name a file on the command line with an expression like -DATa1=myfile.dat. For more information see Chapter 4, Using Data Files in the User's Guide.

The translation of codons to amino acids, the identification of potential start codons and stop codons, and the mappings of one-letter to three-letter amino acid codes are all defined in a translation table in the file translate.txt. If the standard genetic code does not apply to your sequence, you can provide a modified version of this file in your working directory or name an alternative file on the command line with an expression like -TRANSlate=mycode.txt. Translation tables are discussed in more detail in the Data Files manual.

Printed: April 22, 1996 15:54 (1162)