Prerequisites:

• The Introduction to Unix
• Some time with the previous gcg exercises.
• Facility with a good text editor

Learn how to navigate the X interface to the Accelerys GCG package. Through this new interface, explore further the functionality of GCG.

As we have seen recently, gcg provides a complete command line interface. However there are times when it is helpful to be able to visualize the sequences being examined. Seqlab provides this facility.

Seqlab, being a X program requires that you log into locus via a X server. Thus start X upon the Macintosh and use the xterm in order to log into locus:

Logging into Locus

$ ssh -X abelew@locus.umiacs.umd.edu abelew@locus.umiacs.umd.edu's password: abelew has logged on pts/2 from 178-96.mam.umd.edu. $ echo $DISPLAY localhost:11.0 Once logged in, make sure gcg started up successfully. My favorite way to do so is to run genhelp. $ genhelp seqlab

The first thing I did upon my first interaction with seqlab was to check out the options. The most important option there is to make sure that the working directory of seqlab is NOT in your home directory, otherwise seqlab may drive you insane. I created a gcg directory and pointed it there. I also told seqlab to start up in editor mode. Finally, I changed the fonts used by seqlab and restarted.

If we attempt to print on locus, the output of our printing jobs goes to a printer in another building. As a result it is often easier to transfer files from locus to the macintoshes in the owl lab and print the files from here. sftp is one program which allows one to transfer files from one computer to another. An example performed while sitting at a Macintosh in the laboratory.

lfsclab03:~/gcg class$  cd gcg
lfsclab03:~/gcg class$  sftp abelew@locus.umiacs.umd.edu
Connecting to locus.umiacs.umd.edu...
abelew@locus.umiacs.umd.edu's password: 
sftp> cd gcg
I made a gcg directory on the macintosh

sftp>get graphics.ps
graphics.ps                                   100% 5739   402.7KB/s   00:00    
sftp> mget tufa*
tufa.ps                                   100% 5839   302.7KB/s   00:00    
tufa.png                                   100% 5949   408.7KB/s   00:00    
sftp> quit
lfsclab03:~/gcg class$ lpr graphics.ps 

Consider the sequence seqlab1.fasta What can you determine about this sequence? Prepare a brief (ca. 2-3 page) report on the sequence, including a feature map, descriptions of key features, information on the probable origin and identity of the sequence, and any other interesting tidbits you can discern from analysis of the sequence. Your report should be interpretive and well written, and should NOT include printouts of all analyses you performed. Rather it should document the logical process of hypothesis development and testing that you used to study the sequence, present printouts from analyses that provided key insights, and explain your rationale for your analyses and conclusions. This work will be graded on the basis of accuracy, analytical rationale, and clarity of presentation.

Created: Wed Sep 15 00:58:22 EDT 2004 by Charles F. Delwiche
Last modified: Mon Nov 8 15:49:44 EST 2004 by Ashton Trey Belew.