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» A New Similarity Measure among Protein Sequences
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BMCBI
2007
139views more  BMCBI 2007»
13 years 9 months ago
XSTREAM: A practical algorithm for identification and architecture modeling of tandem repeats in protein sequences
Background: Biological sequence repeats arranged in tandem patterns are widespread in DNA and proteins. While many software tools have been designed to detect DNA tandem repeats (...
Aaron M. Newman, James B. Cooper
VLDB
2002
ACM
184views Database» more  VLDB 2002»
14 years 9 months ago
Database indexing for large DNA and protein sequence collections
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...
Ela Hunt, Malcolm P. Atkinson, Robert W. Irving
EDBT
2009
ACM
277views Database» more  EDBT 2009»
14 years 1 months ago
G-hash: towards fast kernel-based similarity search in large graph databases
Structured data including sets, sequences, trees and graphs, pose significant challenges to fundamental aspects of data management such as efficient storage, indexing, and simila...
Xiaohong Wang, Aaron M. Smalter, Jun Huan, Gerald ...
EMNLP
2008
13 years 10 months ago
Learning Graph Walk Based Similarity Measures for Parsed Text
We consider a parsed text corpus as an instance of a labelled directed graph, where nodes represent words and weighted directed edges represent the syntactic relations between the...
Einat Minkov, William W. Cohen
NAR
2002
125views more  NAR 2002»
13 years 8 months ago
ASTRAL compendium enhancements
The ASTRAL compendium provides several databases and tools to aid in the analysis of protein structures, particularly through the use of their sequences. It is partially derived f...
John-Marc Chandonia, Nigel S. Walker, Loredana Lo ...