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» The ed-tree: An Index for Large DNA Sequence Databases
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BMCBI
2002
137views more  BMCBI 2002»
13 years 7 months ago
ORFer - retrieval of protein sequences and open reading frames from GenBank and storage into relational databases or text files
Background: Functional genomics involves the parallel experimentation with large sets of proteins. This requires management of large sets of open reading frames as a prerequisite ...
Konrad Büssow, Steve Hoffmann, Volker Sievert
ICDE
2004
IEEE
139views Database» more  ICDE 2004»
14 years 9 months ago
Engineering a Fast Online Persistent Suffix Tree Construction
Online persistent suffix tree construction has been considered impractical due to its excessive I/O costs. However, these prior studies have not taken into account the effects of ...
Srikanta J. Bedathur, Jayant R. Haritsa
BMCBI
2007
265views more  BMCBI 2007»
13 years 7 months ago
Large scale clustering of protein sequences with FORCE -A layout based heuristic for weighted cluster editing
Background: Detecting groups of functionally related proteins from their amino acid sequence alone has been a long-standing challenge in computational genome research. Several clu...
Tobias Wittkop, Jan Baumbach, Francisco P. Lobo, S...
EDBT
2009
ACM
277views Database» more  EDBT 2009»
14 years 7 days 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 ...
EDBT
2010
ACM
117views Database» more  EDBT 2010»
14 years 2 months ago
Anchoring millions of distinct reads on the human genome within seconds
With the advent of next-generation DNA sequencing machines, there is an increasing need for the development of computational tools that can anchor accurately and expediently the m...
Tien Huynh, Michail Vlachos, Isidore Rigoutsos