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The exact arrangement of the dots is determined before the chip is manufactured. This involves identifying a number of proteins to be represented on the chip and laying them out on the chip surface. This layout is governed by boundary conditions and preferences of the experimental procedures and is not important for the interpretation of the information. 2. Only rudimentary information is attached to each dot. At best, the experiment reveals the complete sequence of the gene or protein. Sometimes, only short segments of the relevant sequence are available.

For most of the century, the structure of protein binding pockets has not been available to the medicinal chemist, so drug design was based on the idea that molecules whose surface is similar in shape and chemical features should bind to the target protein with comparable strength. Thus drug design was based on comparing drug molecules, either intuitively or, more recently, systematically with the computer. As 3D protein structures became available, the so-called rational or structure-based approach to drug development was invented, which exploited this information to develop e€ective drugs.

The object is to interpret experimental data that are generated by sequencing e€orts. e. e. e. the process of piecing together short segments of sequenced DNA to form a contiguous sequence of the genome or chromosome. Layer À1 plays a special role, since it is both a subproblem and an application scenario. The application-oriented character of this problem originates from its close relationship with the applied sequencing procedure. The two competing approaches to sequencing the human genomes, namely whole-genomeshotgun sequencing, as performed by Celera Genomics [4] and BACassembly as performed by the publically funded human genome project [5], which lead to quite di€erent approaches for assembly, have illustrated this point very visibly.

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