How to Handle a Single Sequence

This BioCompanion copy is a demo version . This section describes the methods available to analyse a single sequence with the computer. Algorithms and principles are explained and illustrated with programs from the GCG package. The use of programs in the GCG package as described in this section requires that the setup of the GCG software is performed accordingly. If you have the sequence in electronic form already but did not use it in GCG before, refer to the previous chapters for details.

Prerequisites for all examples and GCG programs

The following description assumes that the set up for the GCG package has already been completed. These sequences used for input must be in GCG format . Use reformat or genmanual sequence_exchange for details on how to convert sequences into GCG format.

Text Output

Many programs ask for an output file. This is mostly letter-by-letter output. You can review this text with the (command line) command more . WPI users (this is an old name, it was renamed to SeqLab in GCG version 9) may use the display function in the "output manager window".

Graphic Output, Launched via Command Line

To display graphics, you need to tell the GCG software that you want to use either display (=screen) or printer (=hardcopy). Command line users must be sure that everything is fine, to achieve this, initialise the display with the command setplot and select the option which seems best suitable to you.

Note that you may choose to use X-Windows as an output device. This will, given the requirements are met, display a separate window for the graphics output of the GCG package. Briefly, you should

• be connected to the Ethernet or similar fast local area network ,

• run an X-Windows capable system (such as a workstation or PC/Mac with suitable X-Server program)

NOTE: A window should come upon your screen after the selection of "X-Windows".

Graphic Output, Launched via SeqLab

WPI users (renamed to SeqLab in GCG version 9) may use the display and print function in the "output manager window".

Notes on Graphics

Check that display or printer work properly when you use them the first time and produce a test graphics with plottest .

NOTE: This is the last time that these details are described. The following chapters of the BioCompanion assume that all these setup operations have been successfully completed.

NOTE: Graphics files may become rather large. If display functionality stops working, make sure that the disk resources are sufficient. Also, if you use SeqLab , have the option 'delete' checked in the "output manager window" so that files get deleted on exit. If you work on the command line, make sure that intermediate .pnt and other files get erased frequently.

GCG graphics may be scaled to allow superimposition of several outputs. For this purpose, the parameter "density" is required. Unless to plan to superimpose output graphics, you may choose the default option if asked.

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