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CSB
2005
IEEE
141views Bioinformatics» more  CSB 2005»
14 years 5 months ago
Reconstructing Phylogenetic Networks Using Maximum Parsimony
Phylogenies—the evolutionary histories of groups of organisms—are one of the most widely used tools throughout the life sciences, as well as objects of research within systema...
Luay Nakhleh, Guohua Jin, Fengmei Zhao, John M. Me...
CSB
2005
IEEE
143views Bioinformatics» more  CSB 2005»
14 years 5 months ago
Analysis of four different sets of predictive features for metalloproteins
Metals bound to the protein are important for functional or structural roles. Despite their importance there is a distinct lack of research for identification of metalloproteins f...
Huseyin Seker, Parvez I. Haris
CSB
2005
IEEE
126views Bioinformatics» more  CSB 2005»
14 years 5 months ago
Visualization of Logic Analysis of Phylogenetic Profiles (LAPP)
Recently Bowers et al. [1] analyzed triplet logic relationships among 4873 Clusters of Orthologous Groups (COGS) from 67 fully sequenced organisms by calculating how well logic re...
Kay A. Robbins, Li Zhao
CSB
2005
IEEE
135views Bioinformatics» more  CSB 2005»
14 years 5 months ago
Inverse Design of Large Molecules using Linear Diophantine Equations
We have previously developed a method [1] for the inverse design of small ligands. This method can be used to design novel compounds with optimized properties (such as drugs) and ...
Shawn Martin, W. Michael Brown, Jean-Loup Faulon, ...
CSB
2005
IEEE
139views Bioinformatics» more  CSB 2005»
14 years 5 months ago
Using Parallel Algorithms for Searching Molecular Sequence Databases
This work presents the development of algorithms for approximate string matching using parallel methods. It intends to do the maximum of molecular sequences comparisons per unity ...
Carla Correa Tavares dos Reis, Rubem P. Mondaini
CSB
2005
IEEE
125views Bioinformatics» more  CSB 2005»
14 years 5 months ago
On Optimizing Distance-Based Similarity Search for Biological Databases
Similarity search leveraging distance-based index structures is increasingly being used for both multimedia and biological database applications. We consider distance-based indexi...
Rui Mao, Weijia Xu, Smriti R. Ramakrishnan, Glen N...
CSB
2005
IEEE
130views Bioinformatics» more  CSB 2005»
14 years 5 months ago
TreeRefiner: A Tool for Refining a Multiple Alignment on a Phylogenetic Tree
We present TreeRefiner, a tool for refining multiple alignments of biological sequences. Given a multiple alignment, a phylogenetic tree, and scoring parameters as input, TreeRefi...
Aswath Manohar, Serafim Batzoglou
CSB
2005
IEEE
166views Bioinformatics» more  CSB 2005»
14 years 5 months ago
Automated Validation of Polymerase Chain Reactions Using Amplicon Melting Curves
PCR, the polymerase chain reaction, is a fundamental tool of molecular biology. Quantitative PCR is the goldstandard methodology for determination of DNA copy numbers, quantitatin...
Tobias P. Mann, Richard Humbert, John A. Stamatoya...
CSB
2005
IEEE
116views Bioinformatics» more  CSB 2005»
14 years 5 months ago
DockingShop: a Tool for Interactive Protein Docking
The molecular docking problem is to determine how molecules interact with other molecules and plays a key role in understanding how cells function. DockingShop is an integrated en...
Ting-Cheng Lu, Jinhui Ding, Silvia N. Crivelli