BITS Meetings' Virtual Library:
Abstracts from Italian Bioinformatics Meetings from 1999 to 2013

766 abstracts overall from 11 distinct proceedings

1. Bortolussi L, Fabris F, Policriti A
Bundled Suffix Trees
Meeting: BITS 2005 - Year: 2005
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Topic: Computer algorithms and applications

Abstract: A Suffix Tree (ST) is a --now classical-- data structure, computable in linear time, which represents the most algorithmically appropriate way to store a string, in order to face problems like the Exact String Matching Problem (ESM) or the Longest Common Exact Substring Problem (LCES). Even if very efficient in solving these problems, the ST data structure suffers from an important drawback, when dealing with an Approximate String Matching Problem (ASM) or with the harder Longest Common Approximate Substring Problem (LCAS), as only exact matching can be used in visiting a ST. In the approximate cases, a suitable notion of distance (most frequently Hamming or Levenshtein distances) must come into play. However, in the literature, there is no universally accepted data structure capable to deal with approximate searches just by performing algorithmic manipulations similar to ST’s. This makes necessary, when using ST's in an approximate context, taking into account errors by using unnatural and complicate strategies, inevitably leading to cumbersome algorithms.

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