MutDB: update on development of tools for the biochemical analysis of genetic variation

Abstract

Understanding how genetic variation affects the molecular function of gene products is an emergent area of bioinformatic research. Here, we present updates to MutDB (http://www.mutdb.org), a tool aiming to aid bioinformatic studies by integrating publicly available databases of human genetic variation with molecular features and clinical phenotype data. MutDB, first developed in 2002, integrates annotated SNPs in dbSNP and amino acid substitutions in Swiss-Prot with protein structural information, links to scores that predict functional disruption and other useful annotations. Though these functional annotations are mainly focused on nonsynonymous SNPs, some information on other SNP types included in dbSNP is also provided. Additionally, we have developed a new functionality that facilitates KEGG pathway visualization of genes containing SNPs and a SNP query tool for visualizing and exporting sets of SNPs that share selected features based on certain filters.

MuPIT interactive: webserver for mapping variant positions to annotated, interactive 3D structures

“…Several excellent web tools are already available for mapping and viewing SNVs on 3D protein structures (Yue et al 2006; Singh et al 2008; Ryan et al 2009; Reva et al 2011). However, MuPIT provides several unique features not found in other tools.…”

“…Thus, users can examine thousands of SNVs from a database or cohort of interest (e.g., ESP6500, COSMIC, TCGA etc), and visualize the relationship between SNVs in 3D (SNVs located close to one another in three-dimensional space may in fact be distant from each other in one-dimensional sequence space). By contrast, SNPs3D (Yue et al 2006) and mutDB (Singh et al 2008) provide the user with a pre-determined list of SNVs in a structure of interest that have been reported in public databases, e.g., NCBI’s dbSNP (Sherry et al 2001) or UniProtKB’s Swiss Variant Pages (UniProt 2012). Similarly, LS-SNP/PDB (Ryan et al 2009) only supports SNVs reported in dbSNP whilst LS-SNP/PDB, Mutation Assessor, and mutDB do not permit viewing of multiple SNVs on a protein structure.…”

“…This application represents a significant improvement on existing web tools (Yue et al 2006; Singh et al 2008; Reva et al 2011) designed to map and visualize SNVs on protein structure in terms of (i) ease of use, (ii) interactive and customizable display, (iii) ability to map multiple mutations onto a single structure in order to visualize clustering patterns, and (iv) visualization of the three-dimensional distances between mutations and position-specific annotations.…”

Annotating Mutational Effects on Proteins and Protein Interactions: Designing Novel and Revisiting Existing Protocols

“…The information on location, tissue type, and frequency of somatic mutations in tumor samples together with the cancer type can be obtained from COSMIC[16] and TCGA databases [17], while other resources, for instance, MutDB [18] and SwissVar [19], integrate the data on germline and somatic mutations for specific genes and diseases.…”

AJAX Interface: A Breakthrough in Bioinformatics Web Applications

“…Using AJAX, this database has successfully enhanced the speed of data exchange with the server. 20 Whereas, AVIS-AJAX viewer of interactive signaling networks [http://actin.pharm.mssm.edu/AVIS2], a google gadget compatible web-based viewer of interactive cell signaling networks have employed AJAX with the usage of the libraries GraphViz, ImageMagic (PerlMagic) and overLib to increase its capability of visualizing the text-based signaling networks in no time. 21 Bobby-Joe Breitkreutz and his group have developed the Biological General Repository for Interaction Datasets (BioGRID) database (http://www.thebiogrid.org) to house and distribute collections of protein and genetic interactions from major model organism species.…”