Toembl

• TOEMBL
  • FUNCTION
  • DESCRIPTION
  • AUTHOR
  • EXAMPLE
  • OUTPUT
  • INPUT FILE
  • COMMAND-LINE SUMMARY

TOEMBL

FUNCTION

ToEmbl is a simple utility program that reads an EMBL entry from a GCG sequence database, and writes it out in EMBL flat file format.

DESCRIPTION

ToEmbl is a simple program that reads an entry from the EMBL database, and writes an EMBL format flat file.

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 ToEmbl

  
  
  % toembl
  
   TOEMBL uses any sequences
  
   TOEMBL of what sequence(s) ?  Em:EcLaci
  
            Start (* 1 *) ?
           End (* 1113 *) ?
         Reverse (* No *) ?
  
   What should I call the output file (* eclaci.em *) ?
  
   ECLACI 1113 characters.
  
  %
  

OUTPUT

The output from ToEmbl is a text file in EMBL format.

  
  
  ID   ECLACI     standard; DNA; PRO; 1113 BP.
  XX
  AC   V00294;
  XX
  DT   09-JUN-1982 (Rel. 01, Created)
  DT   30-NOV-1990 (Rel. 26, Last updated, Version 1)
  XX
  DE   E. coli laci gene (codes for the lac repressor).
  
      ////////////////////////////////////////////////
  
  SQ   Sequence 1113 BP; 249 A; 304 C; 322 G; 238 T; 0 other;
  ccggaagaga gtcaattcag ggtggtgaat gtgaaaccag taacgttata cgatgtcgca   60
  gagtatgccg gtgtctctta tcagaccgtt tcccgcgtgg tgaaccaggc cagccacgtt  120
  
      ////////////////////////////////////////////////
  
  gcgcccaata cgcaaaccgc ctctccccgc gcgttggccg attcattaat gcagctggca 1080
  cgacaggttt cccgactgga aagcgggcag tga                              1113
  //
  

INPUT FILE

The input file for ToEmbl is an EMBL entry in a GCG sequence database.

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: % toembl [-INfile=]Em:Eclaci -Default
  
  Prompted Parameters:
  
  -BEGin=1 -END=1289      Range of interest
  -NOREVerse              Sequence direction
  -ACNumber               Use accession number in output filename
  -OUTfile=eclaci.em      Output file
  

Printed: April 22, 1996 15:56 (1162)