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

Organisation of the gap4 Manual

The main body of the gap4 manual is divided, where possible, into sections covering related topics. If appropriate, these sections commence with an overview of the functions they contain. After the Introduction, the manual contains chapters on some important components of the user interface: the Contig Selector (see section Contig Selector), the Contig Comparator (see section Contig Comparator), and then, in the chapter on Contig Overviews (see section Contig Overviews) we describe the Template Display (see section Template Display), and its subcomponents the Stop Codon Plot (see section Stop Codon Map), and the Restriction Enzyme Plot (see section Restriction Enzyme Search).

Then there is a long chapter on the powerful Contig Editor (see section Editor introduction), followed by a chapter describing the many assembly engines and assembly modes which gap4 can offer (see section Assembly Introduction).

Gap4 contains functions to use the data in an assembly database to find the left to right order of contigs, and to compare their consensus sequences to look for joins that may have been missed during assembly. A "read-pair" is obtained by sequencing a DNA template (or "insert") from both ends: we then know the relative orientations of the two readings, and if we know the approximate template length, we know how far apart they should be after assembly. The next chapter is on the use of read-pair data for ordering contigs and checking assemblies and on the use of consensus comparisons for finding joins (see section Ordering and Joining Contigs).

The next chapter is on checking assemblies and removing readings (see section Checking Assemblies and Removing Readings). The following chapter describes gap4's methods for suggesting experiments for helping to finish a sequencing project (see section Finishing Experiments). Then we describe the various consensus calculation algorithms, and the options for creating consensus sequence files (see section The Consensus Calculation). Next is the description of a set of miscellaneous functions (see section Miscellaneous functions), followed by chapters on the Results Manager (see section Results Manager), Lists (see section Lists Introduction), Notes (see section Notes), Configuring gap4 (see section Options Menu), gap4 Database Files (see section Gap Database Files), Converting Old Databases (see section Converting Old Databases), Checking Databases for corruptions (see section Check Database) and Doctoring corrupted databases (see section Doctor database).

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