Toprimer

• TOPRIMER
  • FUNCTION
  • DESCRIPTION
  • AUTHOR
  • EXAMPLE
  • INPUT FILE
  • OUTPUT FILE

TOPRIMER

FUNCTION

ToPrimer formats a GCG sequence file into a PRIMER compatible file.

DESCRIPTION

ToPrimer reformats a GCG sequence into the format required by the program PRIMER. The complete reference follows: PRIMER: A Computer Program for Automatically Selecting PCR Primers Version 0.5, May 1991 by Stephen E. Lincoln, Mark J. Daly, and Eric S. Lander MIT Center for Genome Research and Whitehead Institute for Biomedical Research, Nine Cambridge Center, Cambridge, Massachusetts 02142

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).

EXAMPLE

Here is a sample session of ToPrimer

  
  
  % toprimer
  
   TOPRIMER uses DNA sequence data
  
   TOPRIMER of what sequence ? amir.seq
  
   What should I call the output file (* amir.prm *) ?
  
  %
  

INPUT FILE

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

OUTPUT FILE

Here is some of the output file from the above session:

  
  
  *sequence: Amir
  ATCGATGCGC GCGGCGTGTT CCAGGTCCGC TGGCAGTCGC CCGAACCGAT TCGCCCCGAC
  CCTTATGTCG TCGTGCATAA CCTCGACGAC TGGTCCGCCA GCATGGGCGG GGGACCGCTC
  CCATGAGCGC CAACTCGCTG CTCGGCAGCC TGCGCGAGTT GCAGGTGCTG GTCCTCAACC
  CGCCGGGGGA GGTCAGCGAC GCCCTGGTCT TGCAGCTGAT CCGCATCGGT TGTTCGGTGC
  GCCAGTGCTG GCCGCCGCCG GAAGCCTTCG ACGTGCCGGT GGACGTGGTC TTCACCAGCA
  TTTTCCAGAA TGGCCACCAC GACGAGATCG CTGCGCTGCT CGCCGCCGGG ACTCCGCGCA
  CTACCCTGGT GGCGCTGGTG GAGTACGAAA GCCCCGCGGT GCTCTCGCAG ATCATCGAGC
  /////////////////////////////////////////////////////////////////
  
  

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: % toprimer [-INfile=]amir.seq -Default
  
  Prompted Parameters:
  
  [-OUTfile=]amir.prm       output file name
  
  Local Data Files: None
  
  Optional Parameters:
  
  -OPTionsmakes the program ask for further primer
  specific options
  
  

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