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2.1. What is GCG ?

The GCG (or 'Wisconsin') package is a collection of programs used to analyse or manipulate DNA and protein sequence data. The package does not provide a single program with a menu, but maintains a consistent style of presentation between different programs. There is sometimes more than one way of doing a given analysis, as different programs may perform similar tasks.

2.1.1. Program examples

In the examples the words in bold text show what you should enter to run the program and provide it with data. If only part of the example is bold, the bold part is the minimum allowable part that you have to type. Text shown in brackets, between asterisks, indicate the assumed values ('defaults') taken by the program when the return key is pressed without typing anything.

eg:

$ Bestfit

BESTFIT explains in a few words what it does and how to use it.

BESTFIT between what sequence 1 ? Myfrog.seq

Begin (* 1 *) ? 9000
End (* 13059 *) ?
Reverse (* No *) ?

and what sequence 2 (* Myfrog.seq *) Anotherfrog.seq

Begin (* 1 *) ?
End (* 5050 *) ? 4050
Reverse (* No *) ? Yes

What should I call the output file (* Myfrog.Bestfit *) ?

2.1.2. Command line modifiers

Almost every GCG program can be given instructions on the command line, instead of using the prompts. To do the same as the previous example entirely on the command line:

$ Bestfit/infile1=myfrog.seq/infile2=anotherfrog.seq/-
$-Begin1=9000/end2=4050/rev2/default

'Infile' specified the input file names. Begin and end specified part of the sequence, rather than use the full sequence. rev2 informed BESTFIT to take the reverse complement of the second sequence. The 'default' modifier states that all other default values are acceptable. ('-' is the VMS "command continued on next line" symbol)

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