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 - 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 - 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 - 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 - 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 - 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 - 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 - 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 - Motivation: Systematic analysis of connection between proteins, their cellular function and phenotypic manifestations in disease is a central problem of biological and clinical research.

De novo computational prediction of non-coding RNA genes in prokaryotic genomes - Motivation: The computational identification of non-coding RNA (ncRNA) genes represents one of the most important and challenging problems in computational biology.