Efficient mapping of large cdna/EST databases to genomes: A comparison of two different strategies
This paper presents a comparison of two strategies for cDNA/EST mapping: The seed-and-extend strategy and the fragment-chaining strategy. We derive theoretical results on the statistics of fragments of type maximal exact match. Moreover, we present efficient fragment-chaining algorithms that are simpler than previous ones. In experiments, we compared our implementation of the fragment-chaining strategy with the seed-and-extend strategy implemented in the software tool BLAT.
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