CENTER for MOLECULAR MEDICINE & GENETICS Wayne State University School of Medicine

SeqWeb is the Web based interface for operating the GCG programs.

BASIC TOOLS NEEDED

To complete this tuturial, you will need a PC, Mac, or UNIX
workstation connected to the network, with Netscape 4.0 or 
higher (Internet Explorer is not recommended).

DOCUMENTATION

The SeqWeb help pages are available at: 
http://cmb.biosci.wayne.edu:8080/help/,

and a quickstart overview is available at: 
http://cmb.biosci.wayne.edu:8080/help/quick_start.html.

Both are password protected.

Complete documentation in PDF format is available at:
http://www.genetics.wayne.edu/gcg/pdfdocs/pdfdocs.html,
which is readable only from the WSU campus.

CONNECT TO THE SEQWEB SERVER

Start Netscape and connect to the SeqWeb server at:
http://www.genetics.wayne.edu/gcg/seqweb.html.  Then
click the SeqWeb logo icon to enter SeqWeb.  A login 
screen prompts for a userid and password.  

SELECT THE MAP PROGRAM

Once logged in, the main SeqWeb screen appears.  Click the 
Index button on the Contents frame at the left of the screen 
to reveal all GCG programs available.  

Scroll down the Index until Map is shown, then click on the 
Nucleic button, which opens the Map program in the Work Area 
at the right.  

Click the little book icon in the upper right to open the 
help documentation for the Map program.  Close the help window.

RETRIEVE THE M13MP18 SEQUENCE FROM THE DATABASE

Click the Databases button, which opens the Add from Databases 
screen.  On the Database pull down menu, select Synthetic.  In 
the Sequence locus name or accession number text box, type 
m13mp18, then click on OK.  

On the screen that comes back, select the gb_sy:m13mp18 entry 
by clicking the check box next to it, then click on Add Selected.  
Click on Close to dismiss the window.  The gb_sy:m13mp18 sequence 
will have been added to the Input Sequence list in the Map program 
frame.  

RUN THE MAP PROGRAM ON THE M13MP18 SEQUENCE

If it's not already highlighted, click the gb_sy:m13mp18 sequence 
in the list to select it.  Various options for running the program 
are available, but for this tutorial, just click on the Run button 
to submit the job with all default parameters.  

EAXAMINE THE MAP RESULTS

The results appear on the screen, and will contain both strands of 
the DNA sequence, with positions of the cutting sites of the known 
restriction enzymes indicated above the DNA sequence, and with the 
amino acid single letter codes for the translated reading frames 
listed below the DNA sequence.

The results can be printed, or they can be saved onto the user's PC 
hard disk as either HTML or plain text.  The results are also saved 
on the server's hard disk in a file with a name similar to 
m13mp18_map_14885.htm, which can be retrieved later in the SeqWeb 
Results Manager (see below).  

The input sequence file, gb_sy:m13mp18, can be viewed by clicking 
on the link near the top of the results screen, or by scrolling 
through the sequence box near the bottom of the results screen.

MANAGE SEQUENCE AND RESULTS FILES

Click the Sequence Mangager button.  The sequences that you have 
loaded into SeqWeb appear in a scrolling list.  Various functions 
such as editing, renaming, deleting, etc. are available.

Click the Results Manager Button.  The files resulting from the 
programs you have run in SeqWeb appear in a scolling list. Options
include viewing them, saving them to your PC hard disk, and 
deleting them.

Note that it is also possible to upload sequence files from your PC
hard drive to SeqWeb, or to copy and paste sequences into SeqWeb.

Click the SeqWeb button to return to the main SeqWeb window.

LOGOUT FROM SEQWEB

Unfortunately, there is no logout button in SeqWeb.  Therefore, it 
is very important that you close your browser after using SeqWeb, 
otherwise someone else could use your account.

Send comments to: dwomble@genetics.wayne.edu

Copyright © 2003, David D. Womble.