Checklen

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

CHECKLEN

FUNCTION

CheckLen calculates five checksums and the sequence length for each entry in a database, and writes them to a file for use in a quick cross check for identical sequences.

DESCRIPTION

CheckLen is one of the programs used to generate the PirOnly database by comparison of SwissProt and Pir entries.

The program does not prompt for values, so everything must be specified on the command line. See the PirOnly documentation for more details of the procedure.

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 CheckLen

  
  
  % checklen SwissProt:* sw.checklen
  
  %
  

OUTPUT

The output from CheckLen is a file containing seven columns. These are five checksums with roots of 57 (the GCG standard checksum), 59, 61, 67 and 71, the length of the sequence and the entry name. The default output filename is simply checklen.checklen.

The example below shows part of the output from a run on the SwissProt database.

  
  
    2611  2810  8003  3343  5949     924 SW:104K_THEPA
    7271  3493   445  4394  3451      75 SW:10KD_VIGUN
    5661  7930  3625  7007  7925     296 SW:110K_PLAKN
719  6538  4802  3682  2369     493 SW:11S3_HELAN
    6954  9062  9203  3585  1668     480 SW:11SB_CUCMA
    4748  1723  5391  1375  1723    1299 SW:120K_RICRI
  
 //////////////////////////////////////////
  
  

INPUT FILE

The input for CheckLen is a GCG sequence database wildcard.

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: % checklen [-INfile=]Sw:* -Default
  
  Prompted Parameters:
  [-OUTfile=]checklen.checklen  Output file
  

Printed: April 22, 1996 15:52 (1162)