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Copyright (C) 1999-2002, Medical Research Council, Laboratory of Molecular Biology.

Organisation of the Pregap4 Manual

Pregap4 is a relatively simple program to use. It is also very flexible and extendable, and so much of the manual is taken up by explaining to programmers and system managers how it can be configured. The average user need not be concerned with these details.

The Introductory section of the manual is meant to give an overview of the program: what it is for, the files it uses and functions it performs, and how to use it. It is very important for all users to have a basic understanding of the files used by pregap4 and the processes through which it can pass their data (see section Summary of the Files used and the Processing Steps). The next section of the Introduction (see section Pregap4 Menus) tabulates the program's menus. This is followed by an overview of the pregap4 user interface (see section Introduction to the Pregap4 User Interface) which should give a clear idea of how to actually use the program, and concludes the introductory section.

More detail about how to define the set of files to be processed (see section Specifying Files to Process) is followed by a section showing how to run pregap4 and giving examples of its use (see section Running Pregap4). This is followed by notes on non-interactive processing (see section Non Interactive Processing) and details of the command line arguments that can be used (see section Command line arguments). Next are sections on configuring the pregap4 user interface (see section Configuring the Pregap4 User Interface).

The next part of the manual describes how to use the Configure Modules Window to select the modules to apply and to set their parameters (see section Configuring Modules). This is one of the longest and most detailed parts of the manual in that it describes how to configure all the current possible modules, many of which will not be available at all sites, and several of which perform identical functions. Obviously, only the entries which describe the functions that are available at a site, are of interest.

One of the important tasks of pregap4 is to make sure that each reading's Experiment file contains all the information needed by gap4 to ensure the accuracy of the final consensus sequence and to make the project proceed as efficiently as possible. Pregap4 provides several methods for sourcing this information. One of these, as for example employed at the Sanger Centre in the UK, is to encode some information about a reading in its reading name. Pregap4 contains flexible mechanisms to enable a variety of the "Naming schemes" or "Naming conventions" to be used as a source of information to augment the Experiment files (see section Pregap4 Naming Schemes). Alternatively pregap4 can use simple text databases as an information source (see section Information Sources), or the user can set up some Experiment file record types for use with a batch of readings (see section Experiment file format record types).

The rest of the manual deals with increasingly complicated matters, and the average user should never need to consult these sections. First there is a section on adding an removing modules (see section Adding and Removing Modules). This describes how to control the list of modules which appear in the Configure Modules Window. The package is usually shipped with this list set to contain more modules than are likely to be available at any one site and so it might be found useful to remove those that are not available.

The next two sections, as their names imply, are for programmers only (see section Low Level Pregap4 Configuration) and (see section Writing New Modules).

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