Gesellschaft für Informatik e.V.

Lecture Notes in Informatics

German Conference on Bioinformatics 2005 (GCB 2005), 5.-7. October 2005, Hamburg, Germany P-71, 29-43 (2005).



Andrew Torda, Stefan Kurtz, Matthias Rarey (eds.)


Efficient mapping of large cdna/EST databases to genomes: A comparison of two different strategies

Christian Wawra , Mohamed I. Abouelhoda and Enno Ohlebusch


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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ISBN 3-88579-400-4

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