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» A polyhedral approach to sequence alignment problems
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CORR
2008
Springer
71views Education» more  CORR 2008»
14 years 9 months ago
Problem Solving and Complex Systems
The observation and modeling of natural Complex Systems (CSs) like the human nervous system, the evolution or the weather, allows the definition of special abilities and models re...
Frédéric Guinand, Yoann Pigné
BMCBI
2008
86views more  BMCBI 2008»
14 years 9 months ago
Subfamily specific conservation profiles for proteins based on n-gram patterns
Background: A new algorithm has been developed for generating conservation profiles that reflect the evolutionary history of the subfamily associated with a query sequence. It is ...
John K. Vries, Xiong Liu
BIBE
2008
IEEE
142views Bioinformatics» more  BIBE 2008»
15 years 4 months ago
Optimizing performance, cost, and sensitivity in pairwise sequence search on a cluster of PlayStations
— The Smith-Waterman algorithm is a dynamic programming method for determining optimal local alignments between nucleotide or protein sequences. However, it suffers from quadrati...
Ashwin M. Aji, Wu-chun Feng
ISMB
2001
14 years 11 months ago
Using mixtures of common ancestors for estimating the probabilities of discrete events in biological sequences
Accurately estimating probabilities from observations is important for probabilistic-based approaches to problems in computational biology. In this paper we present a biologically...
Eleazar Eskin, William Noble Grundy, Yoram Singer
JCB
2002
74views more  JCB 2002»
14 years 9 months ago
Using Substitution Matrices to Estimate Probability Distributions for Biological Sequences
Accurately estimating probabilities from observations is important for probabilistic-based approaches to problems in computational biology. In this paper we present a biologically...
Eleazar Eskin, William Stafford Noble, Yoram Singe...