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).


2005


Editors

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


Contents

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

Christian Wawra , Mohamed I. Abouelhoda and Enno Ohlebusch

Abstract


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


Last changed 24.01.2012 21:51:52