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Finishing Experiments

Gap4 contains several functions for helping to select experiments to finish an assembly project. These functions (which are all available from the gap4 Experiments menu) are able to automatically analyse the contigs to find the regions which need attention, and to suggest appropriate experiments.

Prior to performing any experiments it can be worthwhile to try to make the most of the existing data by moving the boundary between the hidden and visible data of readings to cover single stranded readings. (see section Double Strand)

The following "Experiment Suggestion" functions analyse the contigs to find problems, and then suggest the best templates to use for further experiments.

Primers and templates for primer walking experiments can be suggested. (see section Suggest Primers). Sometimes resequencing on a long gel machine will help to fill a single stranded region or join a pair of contigs. (see section Suggest Long Readings). Compressions and stops can be solved by resequencing using an different chemistry. (see section Compressions and Stops). In order to select oligos to use as probes for clones near the ends of contigs a further function is available. (see section Suggest Probes).

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This page is maintained by staden-package. Last generated on 22 October 2002.