In this lecture, we will give a survey of indexing data structures for sequence data, and more specifically full-text indexes, both from theoretical and practical perspective. We start with the classical suffix tree data structure that remains a very popular tool in theoretical studies as well as in some practical applicaitons. We also present two related structures: Directed Acyclic Word Graph (DAWG) and position heap. We then present the suffix array, which is a more space-efficient structure in practice, and elaborate on its relation to suffix trees. Finally, we present a yet more compact data structure – so-called FM-index – based on the combinatorial Burrows-Wheeler transform. FM-index is now becoming a ubiquitous tool in many bioinformatics applications that we illustrate with several examples.
CSEDays. Theory 2014
Ural Federal University, Ekaterinburg, Russia, August 23 - August 25
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| Для меня это была уже третья школа CSEDays. И, как я и ожидал, она оставила очень позитивные эмоции и дала очередной толчок к тому, чтобы сделать что-то грандиозное в мире Computer Science. Так что, лично я считаю, что школа удалась! |
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