ABSTRACT
This chapter describes simulations of the alignment of recombinant lambdoid and cosmid clones by fingerprinting methods. The purpose of the simulation is to compare methods, as realistically as desired, while preparing for the analysis of actual physical mapping data. The chapter begins to "submit" data to the Human Genome Information Resource to exercise its database. The simulation was repeated using 70 and 100 oligonucleotides, 150, 300, 450, and 600 clones. The chapter describes the method for aligning clones based upon oligonucleotide hybridizing sites, proposed by H. Lehrach, comparing its efficacy on actual human deoxyribonucleic acid sequences from GenBank to its efficacy on random, completely uncorrelated sequences. Although different seeds were used, the genomic segment was used for both the H. Lehrach strategy and the LLNL strategy. The user supplies a specification for the genomic segment from which clones are to be generated and arrayed into contigs.
