Torelate

• TORELATE
  • FUNCTION
  • DESCRIPTION
  • AUTHOR
  • EXAMPLE
  • OUTPUT
  • EXAMPLE
  • INPUT FILE
  • COMMAND-LINE SUMMARY
  • LOCAL DATA FILES
  • OPTIONAL PARAMETERS

TORELATE

FUNCTION

ToRelate creates an input file for the NBRF RELATE program.

DESCRIPTION

ToRelate creates an input file for the NBRF Relate program.

AUTHOR

This program was written by Jack A.M. Leunissen (E-mail: jackl@caos.kun.nl; Post: CAOS/CAMM Center, University of Nijmegen, 6525 ED Nijmegen, The Netherlands).

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 ToRelate

  
  
  % torelate
  
   TORELATE uses any sequences
  
   TORELATE of what sequence(s) ?  sw:fos_*
  
   What should I call the output file (* fos*.dat *) ?  fos.dat
  
   FOS_AVINK 322 characters.
   FOS_CHICK 367 characters.
   FOS_HUMAN 380 characters.
   FOS_MOUSE 380 characters.
   FOS_MSVFB 381 characters.
   FOS_RAT 380 characters.
  
   What matrix shall I use (* md *) ?
  
   What segment length (* 25 *) ?
  
   Number of random runs (* 0 *) ?
  
  
  %
  

OUTPUT

The output from ToRelate is a file which can be used together with the NBRF Relate program.

EXAMPLE

Here is the output file from the above example.

  
  
  RELATE of sw:fos_*; February 28, 1995 11:35
  MD
  25
  15,0
  5
  FOS_AVINK=fos.Seq
  FOS_CHICK=fos.Seq
  FOS_HUMAN=fos.Seq
  FOS_MOUSE=fos.Seq
  FOS_MSVFB=fos.Seq
  FOS_RAT=fos.Seq
  

INPUT FILE

The input file for Torelate is a GCG sequence file.

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.

  
  
  Syntax: $ TORELATE [-INfile=]@Pretty.Fil -Default
  
  Required Parameters:
  
  [-OUTfile1=]Relate.Dat  Parameter output file
  -MATrix=                NBRF scoring matrix (UN, UP, GC, MD)
  -SEGment=25             Segment length
  -RANDom=0               Number of random runs
  
  Local Data Files:
  
  None
  
  Optional Parameters:
  
  -OUTfile2=Relate.Seq    Sequence output file
  -SHORT                  Short form of output
  -INTERval=5             Size of the scoring interval
  -TOPUsed=               Number of top scoring comparisons used in statistics
  -TOPDisplayed=          Number of top scoring comparisons that are displayed
  -NODOCumentation        Suppress documentation accompanying each sequence
  

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.

OPTIONAL PARAMETERS

The parameters and switches listed below can be set from the command line. For more information, see "Using Program Parameters" in Chapter 3, Basic Concepts: Using Programs in the GCG User's Guide.

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