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BMCBI
2004
125views more  BMCBI 2004»
13 years 6 months ago
A fast algorithm for determining the best combination of local alignments to a query sequence
Background: Existing sequence alignment algorithms assume that similarities between DNA or amino acid sequences are linearly ordered. That is, stretches of similar nucleotides or ...
Gavin C. Conant, Andreas Wagner
BMCBI
2007
265views more  BMCBI 2007»
13 years 6 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...
ICDE
2006
IEEE
178views Database» more  ICDE 2006»
14 years 8 months ago
Declarative Querying for Biological Sequences
The ongoing revolution in life sciences research is producing vast amounts of genetic and proteomic sequence data. Scientists want to pose increasingly complex queries on this dat...
Sandeep Tata, Jignesh M. Patel, James S. Friedman,...
SDM
2003
SIAM
156views Data Mining» more  SDM 2003»
13 years 8 months ago
Detection of Underrepresented Biological Sequences using Class-Conditional Distribution Models
A labeled sequence data set related to a certain biological property is often biased and, therefore, does not completely capture its diversity in nature. To reduce this sampling b...
Slobodan Vucetic, Dragoljub Pokrajac, Hongbo Xie, ...
CLUSTER
2003
IEEE
14 years 22 hour ago
A Case Study of Parallel I/O for Biological Sequence Search on Linux Clusters
In this paper we analyze the I/O access patterns of a widely-used biological sequence search tool and implement two variations that employ parallel-I/O for data access based on PV...
Yifeng Zhu, Hong Jiang, Xiao Qin, David R. Swanson