Exons:
Relevant bits of information for using the MUSC Shared Resource, 
the BioMolecular Computing Resource (BCR).

Exon_13 The GCG editors.

SEQED, LINEUP, GELASSEMBLE

SEQED is the principle editor for the GCG system. It was  based on 
VAX VMS editors.  The command:

SEQED filename 

will open "filename" IF it exists and place the cursor at the COOH or 3' 
end of the sequence. If "filename" does not exist, then SEQED opens 
a new sequence and places the cursor at the beginning of the header 
field.  Here one is expected to enter the origin, date, and any other 
useful archive information about the sequence.
To exit the header and begin entering the sequence proper type 
control-D.
This places the cursor at position 1 and sequence entry may begin.

Cursor movement within the sequence proper is as follows:
Control-E moves to the extreme 5' end.
Control-H moves to the extreme 3' end ( ie, left or right).
Shift > moves 50 to the right.
Shift < moves 50 to the left.
To search for a pattern like ATGCG use "/ATGCG" and the cursor will 
move to the 5' end of the pattern if it is located.

To exit the edit mode type control-D again.
This places the  cursor in the field below the sequence to the right of a 
colon.
Typing "help" at this point will start the on-line help
Typing "header" will put the cursor back in the header region to edit the 
header.
Typing "quit" will exit without saving changes.
Typing "exit" will save any changes and exit  SEQED.
Typing "s,f write filename"  will write a portion of the sequence to the 
indicated file.

LINEUP is a multiple sequence editor. Lineup does not create a 
multiple alignment. You may use LINEUP to enter individual 
sequences, then manually align them. You may use LINEUP to 
enter a Multiple Sequence File (MSF) of the sort produced by 
PILEUP ( you must use the "-msf" option to enter an MSF). Once 
entered the file may be altered manually.

The cursor commands are identical with SEQED except that the Up 
and Down arrows now have meaning and there is no header editing 
mode. Control-D gets to the command mode. In the command mode:
Typing "help" at this point will start the on-line help
Typing  "x,y new" will open a space for a new sequence in row "y" and 
place the cursor at column position "x". You are then prompted for a 
name for the
new sequence. Typing  "s,f consensus" will calculate a consensus 
between the indicated start and finish positions and place the sequence
 in the newly opened row. LINEUP uses a different procedure for 
calculating consensus than the PRETTY program .

GELASSEMBLE is the multiple sequence editor for the fragment 
assembly process of GCG. GELASSEMBLE displays the alignments 
produced by GELMERGE. Individual contiguous regions (CONTIGS)
(assuming a collection of fragments were not assembled into one 
CONTIG) may be previewed by successive typing of the arrow keys. 
Loading a specific contig may be accomplished by typing control-k. 
Once loaded, movement around the alignment is accomplished as 
with SEQED and LINEUP. Control-D gets to the command mode. 
In the command mode:
Typing "help" at this point will start the on-line help