BMCBI
2011
13 years 4 months ago
2011
Background: The secondary structure of RNA molecules is intimately related to their function and often more conserved than the sequence. Hence, the important task of searching dat...
SODA
1990
ACM
14 years 1 months ago
1990
ACM
A new and conceptually simple data structure, called a suffix array, for on-line string searches is introduced in this paper. Constructing and querying suffix arrays is reduced to...
ISMB
2000
14 years 1 months ago
2000
Position-specific scoring matrices have been used extensively to recognize highly conserved protein regions. We present a method for accelerating these searches using a suffix tre...
ACMSE
2006
ACM
14 years 2 months ago
2006
ACM
A code clone represents a sequence of statements that are duplicated in multiple locations of a program. Clones often arise in source code as a result of multiple cut/paste operat...
ESA
1998
Springer
14 years 4 months ago
1998
Springer
Information retrieval and data compression are the two main application areas where the rich theory of string algorithmics plays a fundamental role. In this paper, we consider one ...
CIKM
2005
Springer
14 years 6 months ago
2005
Springer
We study suitable indexing techniques to support efficient exact match search in large biological sequence databases. We propose a suffix tree (ST) representation, called STA-DF, ...
VLDB
2005
ACM
15 years 20 days ago
2005
ACM
121
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VLDB
2002
ACM
15 years 20 days ago
2002
ACM
Our aim is to develop new database technologies for the approximate matching of unstructured string data using indexes. We explore the potential of the suffix tree data structure i...
RECOMB
2009
Springer
15 years 1 months ago
2009
Springer
A repetitive sequence collection is one where portions of a base sequence of length n are repeated many times with small variations, forming a collection of total length N. Example...
ICML
2006
IEEE
15 years 1 months ago
2006
IEEE
String kernels which compare the set of all common substrings between two given strings have recently been proposed by Vishwanathan & Smola (2004). Surprisingly, these kernels...