Contig Graph Tool: a graphical interface for contig physical map assembly

A contig physical map of a chromosome is a collection of DNA clones organized into ordered, overlapping sets called contigs which cover contiguous regions of the chromosome. By exploring contig properties using a graph representation, the Contig Graph Tool (CGT) user can interactively detect and correct inconsistencies in a contig´s clone content and overlap constraints. Production physical mapping of chromosomes requires electronic databases to manage large volumes of experimental and derived data. The challenge for CGT is to support database interaction and editable visualization to users without compromising database integrity or limiting user investigation. This required several novel interface techniques. The author describes the representation of contigs as graphs and motivates the use of graph properties to detect problems in sets of overlaps. He considers operational requirements for contig editing, i.e. trial-and-error investigation in an experimental environment that requires database management reliability. How these requirements were met is discussed, and the CGT is described. CGT is compared to previous work, its major limitations are considered, and enhancements are proposed.