LocusFocus is a web application to facilitate the exploration of a GWAS signal at a particular locus of the genome and its degree of colocalization with any SNP-level association data (e.g. expression quantitative trait loci for genes within +/- 1Mbp in the relevant GTEx tissues selected).
The goal of AGILE (Assembled Genome minIng pipeLinE) is to mine and annotate genes from a target genome using a set of reference genes from a closely related taxon.
Apollo is the first instantaneous, collaborative genomic annotation editor available on the Web.
Web Apollo is designed to support geographically dispersed researchers, and the work of a distributed community is coordinated through automatic synchronization: all edits in one client are instantly pushed to all other clients, allowing users to see annotation updates from collaborators in real-time during the editing process.
CHASM is a method that predicts the functional significance of somatic missense mutations observed in the genomes of cancer cells, allowing mutations to be prioritized in subsequent functional studies, based on the probability that they give the cells a selective survival advantage.
CHASMplus is a machine learning method that accurately distinguishes between driver and passenger missense mutations, even for those found at low frequencies or are cancer type-specific.
The POLYVIEW-2D protein structure visualization server can be used to generate amino acid sequence annotations, such as secondary structure, relative solvent accessibility, evolutionary conservation, and physico-chemical property profiles. It can also be used to identify residues involved in protein-protein interactions and highlight other important sites and motifs.
POLYVIEW-3D is a web-based tool for macromolecular structure visualization and analysis. In particular, it provides a wide array of options for automated structural and functional analysis of proteins and their complexes. This tutorial aims to describe and illustrate the available rendering options and annotation capabilities of POLYVIEW-3D.
POLYVIEW-MM (Molecular Motion) enables animation of trajectories generated by Molecular Dynamics and related simulation techniques, as well as visualization of alternative conformers, e.g., obtained as a result of protein structure prediction methods or small molecule docking, using an intuitive web-based interface.
ANNIE is a comprehensive de novo protein annotation system that integrates a large number of indispensable algorithms used in everyday sequence analytic work.
Nucleic Acids Res. 2009 Jul;37(Web Server issue):W435-40. doi: 10.1093/nar/gkp254. Epub 2009 Apr 23. ANNIE: integrated de novo protein sequence annotation.
Ooi HS, Kwo CY, Wildpaner M, Sirota FL, Eisenhaber B, Maurer-Stroh S, Wong WC, Schleiffer A, Eisenhaber F, Schneider G
GenomeRunner is a tool for automating genome exploration. It performs annotation and enrichment analyses of user-provided genomic regions (SNPs, ChIP-seq binding sites etc.) against >6,000 (human genome) epigenomic features available from the UCSC genome browser.
