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

EXON_10: Fragment assembly: GCG Software to help manage a 
sequencing project.

The "GEL" programs help the user manage a sequencing project.

The basic process is as follows.

1. Execute the command "gelstart". Gelstart prompts you for a project 
name and asks what vector sequences are  to be highlighted and 
what restriction sites to highlight. The vector sequence must be in the 
current directory or you must include a path to the file. The restriction 
sites must be entered literally, ie you may not enter ECORI for example. 
Gelstart creates a number of directories. If you wish to delete a 
sequence assembly project that is already built, the option to add   
is "-delete". You are then prompted for a name and asked to confirm 
your desire to delete. This "-delete" option is very useful for clean-up 
and for removing aborted projects.

2. Execute the "gelenter" command. Without options this command 
opens an editor and prompts for a sequence. AT THIS TIME ONLY, 
he indicated restriction sites and vector sequences are highlighted 
with reverse video (but see below in gelmerge). An easier way to enter 
sequences into the GELsystem is to use the option "-enter=N*". This 
command causes the computer to collect all files which begin with the 
letter capitol N. Clearly,  naming sequences with repetitive prefixes 
(or suffixes) will be an aid. The problem is that highlighting does NOT 
work when the "-enter" option is evoked.

3. Execute the command "gelmerge". At this time if you use the option 
"-excise" and  "-report=my.report" then gelmerge will scan your project
sequences for vector fragments which you told it about at the gelstart  
step. It will then excise any finds, and write in the text file "my.report" 
(obviously you would enter your own name for the report). Gelenter 
reads the (possibly modified)  files, aligns them, and computes a series 
of contigs. Under some circumstances, a large number of sequences 
may be coalesced into a single contig. More often there will remain 
several contigs but fewer than the total number of input sequences.

4. When you execute the "gelassemble" command, the program takes
 its information from gelmerge and "presents" the contig(s)  in the 
format of a GCG text editor. The first  contig is presented at startup. 
This presentation is NOT in the editable mode.You may 'load' this 
contig by typing "control-k" or you may elect to view another contig. 
The right arrow will show the next contig in the stack and so forth.
You may load any contig with control-k. Once a contig is loaded, 
the system enters the insert or screen mode. There are two modes. 
Command mode (with the colon ":". At this point you may get on-line 
help by typing 'help') and Screen mode. Typing ctrl-d toggles back 
and forth between these modes.  In screen mode, ctrl-H moves to the 
5' end while ctrl-e moves to the 3' end of the sequence. At the bottom 
of the screen is the calculated consensus. Upper case letters denote 
full consensus. Lowercase letters denote variation. Above the 
consensus are the individual sequences with labels. Within these, any
variance from the consensus is highlighted in reverse video. You may 
search, insert, delete and move any one sequence or any block of
sequences.When you are satisfied with the alignment, shift to the 
command mode (ctrl-d) and type one of the following:
quit  to quit without saving
exit   to quit and save the alterations
meld to save the present contig arragement
s,f write sequence.out This writes the consensus to a sequence file.

You may resume your analysis at any time. Gelstart will recognize 
existing projects and open them for you. You may re-run gelenter, 
gelmerge and gelassemble as often as warranted. 

An example:
Say on the first of March you create a project called IDES. You have 
three sequences: ides1, ides2, and ides3 which may have fragments 
of pBluescript
in them.

gelstart  -vector=pbluescript.seq  ides
gelenter -enter=ides*
gelmerge -excise -report=ides_excise.report

You get two contigs (not a complete assembly)  so you quit

On March 16 you have two new sequences, ides4 and ides5.

gelstart ides  

The system identifies an existing project and opens it.

gelenter -enter=ides*

This adds the new sequences. It will point out that ides1, ides 2, 
and ides3 are repeat names and can only be added once and 
then proceed to add ides4 and ides5.

gelmerge -excise -report=ides_excise_2.report

You create a new report file.

This time you wind up with one contig so you proceed to 
gelassemble  to view the alignments and write out your assembled 
contig.