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CIKM
2005
Springer
16 years 22 hour ago
Exact match search in sequence data using suffix trees
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, ...
Mihail Halachev, Nematollaah Shiri, Anand Thamildu...
BIBE
2003
IEEE
116views Bioinformatics» more  BIBE 2003»
15 years 11 months ago
An Assessment of a Metric Space Database Index to Support Sequence Homology
Hierarchical metric-space clustering methods have been commonly used to organize proteomes into taxonomies. Consequently, it is often anticipated that hierarchical clustering can ...
Rui Mao, Weijia Xu, Neha Singh, Daniel P. Miranker
RECOMB
1997
Springer
15 years 10 months ago
Sequence alignment with tandem duplication
Algorithm development for comparing and aligning biological sequences has, until recently, been based on the SI model of mutational events which assumes that modi cation of sequen...
Gary Benson
SODA
2001
ACM
110views Algorithms» more  SODA 2001»
15 years 7 months ago
Absolute convergence: true trees from short sequences
Fast-converging methods for reconstructing phylogenetic trees require that the sequences characterizing the taxa be of only polynomial length, a major asset in practice, since rea...
Tandy Warnow, Bernard M. E. Moret, Katherine St. J...
KDID
2003
93views Database» more  KDID 2003»
15 years 7 months ago
A Framework for Frequent Sequence Mining under Generalized Regular Expression Constraints
This paper provides a framework for the extraction of frequent sequences satisfying a given regular expression (RE) constraint. We take advantage of the information contained in th...
Hunor Albert-Lorincz, Jean-François Boulica...