Togenbank

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

TOGENBANK

FUNCTION

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

DESCRIPTION

ToGenBank is a simple program that reads an entry from the GenBank database, and writes a GenBank 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 ToGenBank

  
  
  % togenbank
  
   TOGENBANK uses nucleotide sequences
  
   TOGENBANK of what sequence(s) ?  GenBank:EcoTrpr
  
               Start (* 1 *) ?
              End (* 1289 *) ?
            Reverse (* No *) ?
  
   What should I call the output file (* ecotrpr.gb *) ?
  
   ECOTRPR 1289 characters.
  
  %
  

OUTPUT

The output from ToGenBank is a text file in GenBank format.

  
  
  LOCUS       ECOTRPR      1289 bp ds-DNA             BCT       22-SEP-1986
  DEFINITION  E.coli trpR gene coding for the trp operon repressor protein.
  ACCESSION   J01715 V00369
  KEYWORDS    DNA binding protein; repressor; trp repressor; trpR gene.
  SOURCE      Escherichia coli DNA [1],[2] and mRNA [2].
  
      ////////////////////////////////////////////////
  
  BASE COUNT      309 a    352 c    346 g    282 t
  ORIGIN      BamHI site [Nucleic Acids Res. 8, 1551-1560 (1980)]; 99.8 min on K
     1 GGATCCGGAA ACGAATATCA ACATTGGCAC CAGTTACCTG CAATATGTTT
   ATCAGCAGTT
    61 TGGCAATAAT CGTATTTTCT CCTCAGCAGC TTATAACGCC GGACTAGGGC
   GGGTGCGAAC
  
      ////////////////////////////////////////////////
  
  1201 TTTCGTGCGC CAGCGCGCGT TTCCTCACTG CCAAAGGGCT GTTCCGGTAC
   ACCGCTCTCG
  1261 ACGGCAACGG ATGCAATATG GCAGGATCC
  //
  
  

INPUT FILE

The input file for ToGenBank is a GenBank 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: % togenbank [-INfile=]GenBank:EcoTrpr -Default
  
  Prompted Parameters:
  
  -BEGin=1 -END=1289      Range of interest
  -NOREVerse              Sequence direction
  -ACNumber               Use accession number in output filename
  -OUTfile=ecotrpr.gb     Output file
  

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