map and mapplot can be used to map restriction sites and open reading frames on an unknown DNA sequence. mapplot generates a very nice output, but our current setup provides us with only limited printing abilities. map generates an ascii file which can be downloaded, formatted, and printed with a desktop computer.
dotplot can be used to ccompare two seqeunces for repetitive patterns . It works by making a sliding-window comparison between the two sequences.
seqed is a sequence editor that can be used to enter and edit sequences. seqed's interface is derived from that of the unix editor vi. vi takes some getting used to, but is actually kind of nice to use once you know your way around.
Most GCG utilities can be run either via a dialog, or directly from a single command line. The command line interface is faster, but requires a fair familiarity with GCG. To see the command line syntax for any command, consult the GCG manual.
GCG has a number of tools for evaluating the codon usage patterns in DNA sequences. Because coding regions have a distinctive DNA composition, codon usage and GC content can be used to detect open reading frames in a stretch of DNA of unknown function. Species also have distinctive codon usage patterns, so a sequence of unknown origin can sometimes have its source identified by analysis of codon usage, and codon usage can contain hints about the evolutionary history of a gene.
vi has two distinct modes, command mode and insert mode. When you first start vi you will be in command mode. In this mode letters on the keyboard control the movement of the cursor, deletion and manipulation of text, etc. In command mode, what you type on the keyboard is inserted into the file you are editing. Most vi commands involve a single letter command typed in command mode, but some commands are more complex, and require using the status line.
vi is a complex and powerful editor, but it is somewhat difficult to learn because the commands are rather cryptic. The following commands provide a basic introduction. Read the man page or buy a guide book for more detailed information.
h,j,k,l - left, down, up, right
spacebar - right
w - jump forward one word
) - jump to beginning of next sentence
} - jump to next paragraph
/pattern - search forward for pattern
To enter insertion mode, type one of the following single letter commands:
To exit insertion mode, press and release the 'escape' key. This will return you to command mode.