An Editing Environment for DNA Sequence Analysis

This paper presents a computer system for analyzing and annotating large-scale genomic sequences. The core of the system is a multiple-gene structure identi cation program, which predicts the most \probable" gene structures based on the given evidence, including pattern recognition, EST and protein homology information. A graphics-based user interface provides an environment which allows the user to interactively control the evidence to be used in the gene identi cation process. To overcome the computational bottleneck in the database similarity search used in the gene identi cation process, we have developed an e ective way to partition a database into a set of sub-databases of \related" sequences, and reduced the search problem on a large database to a signature identi cation problem and a search problem on a much smaller sub-database. This reduces the number of sequences to be searched from N to O( p N) on average, and hence greatly reduces the search time, where N is the number of sequences in the original database. The system provides the user with the ability to facilitate and modify the analysis and modeling in real time.