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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Всем спасибо! Было круто! Море интересностей, плюшек и интерактива. Регулярные перерывы и кофе-брейки дают возможность хорошенько усвоить материал и коллективно поразмышлять о насущном. Отдельно хочется поблагодарить Есина Антона, Логинова Илью и Пшеничного Дмитрия за отличный курс по маршрутизаторам и хоть и малое, но весьма интересное общение. Жаль что не хватило времени разобраться в некоторых моментах более детально. |
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