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|  University of Hawai'i Manoa |
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| University of Hawai'i Manoa |
The COBRE Bioinformatics Facility at UHM offers access to high speed computer hardware and bioinformatics consultation. Research at the facility includes studying of evolutionary change in emergent dengue viruses associated with increasingly severe epidemics and confirm the impact of these changes in experimental models.
Member:
Baek, Kyungim, Ph.D.
Role:
Assistant Professor, Associate Director, Bioinformatics Core
Member:
Le Pape, Marc, Ph.D
Role:
Associate Director, Bioinformatics Core
Lab contains two of these instruments.
Lab contains two of these instruments.
"The Basic Local Alignment Search Tool (BLAST) finds regions of local similarity between sequences. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance of matches. BLAST can be used to infer functional and evolutionary relationships between sequences as well as help identify members of gene families." iNquiry bioinformatics software suite.
"Lasergene Core Suite is a comprehensive DNA and protein sequence analysis software suite comprised of eight applications which include functions ranging from sequence assembly and SNP detection, to automated virtual cloning and primer design."
"EMBOSS is "The European Molecular Biology Open Software Suite". EMBOSS is a free Open Source software analysis package specially developed for the needs of the molecular biology (e.g. EMBnet) user community. The software automatically copes with data in a variety of formats and even allows transparent retrieval of sequence data from the web. Also, as extensive libraries are provided with the package, it is a platform to allow other scientists to develop and release software in true open source spirit. EMBOSS also integrates a range of currently available packages and tools for sequence analysis into a seamless whole. EMBOSS breaks the historical trend towards commercial software packages."
iNquiry bioinformatics software suite. "Multiple alignment of nucleic acid and protein sequences."
"FileMaker Pro is powerful, easy-to-use database software.
Flow cytometry data and statistical analysis software.
"GeneSpring GX provides powerful, accessible statistical tools for fast visualization and analysis of expression and genomic structural variation data. Designed specifically for the needs of biologists, GeneSpring GX offers an interactive desktop computing environment that promotes investigation and enables understanding of microarray data within a biological context."
iNquiry bioinformatics software suite.
"Glimmer is a system for finding genes in microbial DNA, especially the genomes of bacteria, archaea, and viruses. Glimmer (Gene Locator and Interpolated Markov ModelER) uses interpolated Markov models (IMMs) to identify the coding regions and distinguish them from noncoding DNA."
"GraphPad Prism is a powerful combination of basic biostatistics, curve fitting and scientific graphing in one comprehensive program....
Designed for the practical scientist, Prism does not expect you to be a statistician. It guides you through each analysis - giving you as much help as you need - and tracks and organizes your work like no other program available."
iNquiry bioinformatics software suite.
"Almost any workflow involves computing results, and that's what Mathematica does—from building a hedge fund trading website or publishing interactive engineering textbooks to developing embedded image recognition algorithms or teaching calculus.
Mathematica is renowned as the world's ultimate application for computations. But it's much more—it's the only development platform fully integrating computation into complete workflows, moving you seamlessly from initial ideas all the way to deployed individual or enterprise solutions."
"MrBayes is a program for the Bayesian estimation of phylogeny. Bayesian inference of phylogeny is based upon a quantity called the posterior probability distribution of trees, which is the probability of a tree conditioned on the observations. The conditioning is accomplished using Bayes's theorem. The posterior probability distribution of trees is impossible to calculate analytically; instead, MrBayes uses a simulation technique called Markov chain Monte Carlo (or MCMC) to approximate the posterior probabilities of trees."
Software for inferring and interpreting phylogenetic trees.
"PHYLIP is a free package of programs for inferring phylogenies."
"R is a free software environment for statistical computing and graphics."
Website includes download, demos, and support.
"DNA sequence assembly and analysis software."