Genome Analysis: Pattern Search in Biological Macromolecules

Biological sequence data analysis has developed into an inevitable tool for macromolecular biology, key to any detailed understanding of the living cell. A brief survey on the biological macromolecules and their function is given. Sequence data analysis is introduced as a basic tool for the experimental bench biologist. So far, most queries for such analyses are issued on flat files and static indices. We discuss position tree structures and their potential in sequence data analysis. The hash position tree is introduced as a persistent, dynamic data structure for pattern searches in large sequence databases in biology.

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