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CP
2003
Springer
14 years 25 days ago
A SAT-Based Approach to Multiple Sequence Alignment
Multiple sequence alignment is a central problem in Bioinformatics. A known integer programming approach is to apply branch-and-cut to exponentially large graph-theoretic models. T...
Steven David Prestwich, Desmond G. Higgins, Orla O...
IEEEPACT
2006
IEEE
14 years 1 months ago
Fast, automatic, procedure-level performance tuning
This paper presents an automated performance tuning solution, which partitions a program into a number of tuning sections and finds the best combination of compiler options for e...
Zhelong Pan, Rudolf Eigenmann
ICCAD
1994
IEEE
117views Hardware» more  ICCAD 1994»
13 years 11 months ago
Optimal latch mapping and retiming within a tree
We propose a technology mapping algorithm that takes existing structural technology-mapping algorithms based on dynamic programming [1,3,4] and extends them to retime pipelined cir...
Joel Grodstein, Eric Lehman, Heather Harkness, Her...
BIBM
2007
IEEE
132views Bioinformatics» more  BIBM 2007»
14 years 1 months ago
A Divide-and-Conquer Implementation of Three Sequence Alignment and Ancestor Inference
In this paper, we present an algorithm to simultaneously align three biological sequences with affine gap model and infer their common ancestral sequence. Our algorithm can be fu...
Feng Yue, Jijun Tang
BMCBI
2008
122views more  BMCBI 2008»
13 years 7 months ago
Grammar-based distance in progressive multiple sequence alignment
Background: We propose a multiple sequence alignment (MSA) algorithm and compare the alignment-quality and execution-time of the proposed algorithm with that of existing algorithm...
David J. Russell, Hasan H. Otu, Khalid Sayood