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» Improving EAs for Sequencing Problems
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2000
ACM
156views Algorithms» more  STOC 2000»
15 years 4 months ago
Near optimal multiple alignment within a band in polynomial time
Multiple sequence alignment is a fundamental problem in computational biology. Because of its notorious difficulties, aligning sequences within a constant band (c-diagonal) is a ...
Ming Li, Bin Ma, Lusheng Wang
RECOMB
2006
Springer
16 years 6 days ago
RNA Secondary Structure Prediction Via Energy Density Minimization
Abstract. There is a resurgence of interest in RNA secondary structure prediction problem (a.k.a. the RNA folding problem) due to the discovery of many new families of non-coding R...
Can Alkan, Emre Karakoç, Süleyman Cenk...
BMCBI
2007
109views more  BMCBI 2007»
15 years 1 hour ago
Computational RNA secondary structure design: empirical complexity and improved methods
Background: We investigate the empirical complexity of the RNA secondary structure design problem, that is, the scaling of the typical difficulty of the design task for various cl...
Rosalía Aguirre-Hernández, Holger H....
KELSI
2004
Springer
15 years 5 months ago
Improving Rule Induction Precision for Automated Annotation by Balancing Skewed Data Sets
There is an overwhelming increase in submissions to genomic databases, posing a problem for database maintenance, especially regarding annotation of fields left blank during submi...
Gustavo E. A. P. A. Batista, Maria Carolina Monard...
BMCBI
2005
114views more  BMCBI 2005»
14 years 11 months ago
A new decoding algorithm for hidden Markov models improves the prediction of the topology of all-beta membrane proteins
Background: Structure prediction of membrane proteins is still a challenging computational problem. Hidden Markov models (HMM) have been successfully applied to the problem of pre...
Piero Fariselli, Pier Luigi Martelli, Rita Casadio