Kabattogcg

• KABATTOGCG
  • FUNCTION
  • DESCRIPTION
  • AUTHOR
  • OUTPUT
  • INPUT FILE
  • COMMAND-LINE SUMMARY
  • LOCAL DATA FILES

KABATTOGCG

FUNCTION

KabatToGCG creates GCG data libraries from Kabat distribution files.

DESCRIPTION

KabatToGcg converts the KABAT immunoglobulin protein database into a sequence database in GCG format.

The Kabat nucleotide sequence database is in GenBank format, and can be converted with the GenBankToGcg program in GCG.

AUTHOR

This program was written by Rodrigo Lopez S. (E-mail: rodrigol@biotek.uio.no; Post: Biotechnology Centre of Oslo, PO Box 1125 Blindern, N-0317 Oslo 3, Norway).

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

OUTPUT

The output from KabatToGcg is a protein sequence database in GCG format.

INPUT FILE

The input for KabatToGcg is the Kabat database KabatP protein sequence distribution files.

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: % kabattogcg [-INfile=]TapeDir:*.seq -Default
  
  Prompted Parameters:
  
  -RELease=1.0             release number (defaults to 1.0)
  -YEAr=90                 release year (defaults to current year)
  -MONth=6                 release month (defaults to current month)
  
  Command Line Options:
  
  [-EXCLude=]embl.exclude  is a file of excluded accession numbers
  [-DIRectory=]dirname     writes in a directory other than GenBankDir
  -NOPURge                 suppresses purging of the index files.
  -NONUMbers               suppresses creation of an accession numbers index file
  -NOSUMmary               suppresses screen summaries
  The following options can be used if there is only one input file:
  
  -NOBINary                stores sequences as ASCII text in the .seq file
  -ISPept                  formats GenPept files
  -LN=KABAT                defines the long name (defaults to output filename)
  -SN=KAB                  defines the short name (defaults to long name)
  -OUTfile=kabat           specifies output file basename (defaults to input
                      file basename)
  
  

LOCAL DATA FILES

None.

Printed: April 22, 1996 15:53 (1162)