ADGO is a web tool that provides composite interpretations for microarray data comparing two sample groups. It also provides composite interpretations and enrichment analysis for lists of genes from diverse sources of biological information.
Alignment of RNA Tertiary Structures (ARTS) is a method for aligning two nucleic acid structures (RNAs or DNAs) and detecting a-priori unknown common substructures.
Asterias is a set of tools for the analyses of high throughput genomic data that includes applications for microarray data normalization, filtering, detection of differential gene expression, class and survival prediction model building, and analysis of array CGH data. Most applications use parallel computing resulting in significant increases in speed.
AUGUSTUS is a eukaryotic gene prediction tool. It can integrate evidence, e.g. from RNA-Seq, ESTs, proteomics, but can also predict genes ab initio. The PPX extension to AUGUSTUS can take a protein sequence multiple sequence alignment as input to find new members of the family in a genome. It can be run through a web interface, or downloaded and run locally.
Bioconductor is an open source and open development software project that aims to provide access to a wide range of powerful statistical and graphical methods for the analysis of genomic data.
BiologicalNetworks allows retrieval, construction, and visualization of biological networks and allows for the analysis of high-throughput expression data by mapping onto network graphs. BiologicalNetworks queries the PathSys system, a combined database of biological pathways, gene regulatory networks, and protein interaction maps.
Bioverse is a system that uses computational techniques to facilitate exploring the relationships between molecular, genomic, proteomic, systems and organismal information.
Composite Module Analyst (CMA) defines promoter models based on the composition of transcription factor binding sites (TFBS) in regulatory sequences for sets of coregulated genes.
DEEP (Differential Expression Effector Prediction) is a tool that can identify effectors of specific expression profiles by combining gene expression data with biological expert knowledge about biomolecular interaction networks (provided by resources like TRANSPATH, for example).
DiANNA (DiAminoacid Neural Network Application) a tool that predicts cysteine states of a protein. It can predict whether a particular cysteine is reduced, is forming a disulfide bond, or is bound to a metallic ligand.
134 Resources
453 Databases
