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BIBM
2008
IEEE
112views Bioinformatics» more  BIBM 2008»
14 years 4 months ago
Fast Alignments of Metabolic Networks
Network alignments are extensively used for comparing, exploring, and predicting biological networks. Existing alignment tools are mostly based on isomorphic and homeomorphic embe...
Qiong Cheng, Piotr Berman, Robert W. Harrison, Ale...
BMCBI
2007
142views more  BMCBI 2007»
13 years 10 months ago
SABERTOOTH: protein structural alignment based on a vectorial structure representation
Background: The task of computing highly accurate structural alignments of proteins in very short computation time is still challenging. This is partly due to the complexity of pr...
Florian Teichert, Ugo Bastolla, Markus Porto
TC
2010
13 years 8 months ago
Network-on-Chip Hardware Accelerators for Biological Sequence Alignment
—The most pervasive compute operation carried out in almost all bioinformatics applications is pairwise sequence homology detection (or sequence alignment). Due to exponentially ...
Souradip Sarkar, Gaurav Ramesh Kulkarni, Partha Pr...
KCAP
2011
ACM
13 years 27 days ago
Let's agree to disagree: on the evaluation of vocabulary alignment
Gold standard mappings created by experts are at the core of alignment evaluation. At the same time, the process of manual evaluation is rarely discussed. While the practice of ha...
Anna Tordai, Jacco van Ossenbruggen, Guus Schreibe...
PLDI
2004
ACM
14 years 3 months ago
Vectorization for SIMD architectures with alignment constraints
When vectorizing for SIMD architectures that are commonly employed by today’s multimedia extensions, one of the new challenges that arise is the handling of memory alignment. Pr...
Alexandre E. Eichenberger, Peng Wu, Kevin O'Brien