blogs

HTqPCR: high-throughput analysis and visualization of quantitative real-time PCR data in R

HTqPCR: high-throughput analysis and visualization of quantitative real-time PCR data in R - Motivation: Quantitative real-time polymerase chain reaction (qPCR) is routinely used for RNA expression profiling, validation of microarray hybridization data and clinical diagnostic assays.

NAViGaTOR: Network Analysis, Visualization and Graphing Toronto

NAViGaTOR: Network Analysis, Visualization and Graphing Toronto - Summary: NAViGaTOR is a powerful graphing application for the 2D and 3D visualization of biological networks.

Genome analysis with inter-nucleotide distances

Genome analysis with inter-nucleotide distances - Motivation: DNA sequences can be represented by sequences of four symbols, but it is often useful to convert the symbols into real or complex numbers for further analysis.

HHsvm: fast and accurate classification of profile-profile matches identified by HHsearch

HHsvm: fast and accurate classification of profile-profile matches identified by HHsearch - Motivation: Recently developed profile–profile methods rival structural comparisons in their ability to detect homology between distantly related proteins.

A generalized conformational energy function of DNA derived from molecular dynamics simulations

A generalized conformational energy function of DNA derived from molecular dynamics simulations - Proteins recognize DNA sequences by two different mechanisms. The first is direct readout, in which recognition is mediated by direct interactions between the protein and the DNA bases.

Real-time DNA microarray analysis

Real-time DNA microarray analysis - We present a quantification method for affinity-based DNA microarrays which is based on the real-time measurements of hybridization kinetics. This method, i.e.

Lost in translation: an assessment and perspective for computational microRNA target identification

Lost in translation: an assessment and perspective for computational microRNA target identification - MicroRNAs (miRNAs) are a class of short endogenously expressed RNA molecules that regulate gene expression by binding directly to the messenger RNA of protein coding genes.

Next generation software for functional trend analysis

Next generation software for functional trend analysis - Summary: FuncAssociate is a web application that discovers properties enriched in lists of genes or proteins that emerge from large-scale experimentation. Here we describe an updated application with a new interface and several new features.

QuickGO: a web-based tool for Gene Ontology searching

QuickGO: a web-based tool for Gene Ontology searching - Summary: QuickGO is a web-based tool that allows easy browsing of the Gene Ontology (GO) and all associated electronic and manual GO annotations provided by the GO Consortium annotation groups QuickGO has been a popular GO browser for many year

Phenotypic categorization of genetic skin diseases reveals new relations between phenotypes, genes and pathways

Phenotypic categorization of genetic skin diseases reveals new relations between phenotypes, genes and pathways - Motivation: Systematic analysis of connection between proteins, their cellular function and phenotypic manifestations in disease is a central problem of biological and clinical research.