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JAMALAH--a system for the detection of single nucleotide polymorphisms

Dense linkage maps facilitate high resolution mapping, permit epidemiological studies, allow isolation of genes by positional cloning methods, and serve as important frameworks for complete genomic sequencing. As the Human Genome Project moves towards its final stages, scientists have begun to construct a third generation of genetic map, which will eventually consist of thousands of single nucleotide polymorphic markers. The ability to detect these polymorphisms in large scale using new technologies such as the oligonucleotide probe arrays promises to make this new map more powerful than the maps of previous generations. JAMALAH is a prototype software system for rapid detection of potential single nucleotide polymorphisms. The system allows the identification of potential polymorphisms by sequence comparison analysis alone. Its operation requires minimal human intervention, making the system ideal for repeated use. Experimental studies have validated the system's potential and provided incentive for future expansion.