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.
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.
This program was written by Peter Rice (E-mail: firstname.lastname@example.org 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 (email@example.com).
Here is a sample session with CheckLen
% checklen SwissProt:* sw.checklen %
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 //////////////////////////////////////////
The input for CheckLen is a GCG sequence database wildcard.
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)