Skip to main page content
Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2008 Jan;36(Database issue):D815-9.
doi: 10.1093/nar/gkm659. Epub 2007 Sep 7.

MutDB: Update on Development of Tools for the Biochemical Analysis of Genetic Variation

Free PMC article

MutDB: Update on Development of Tools for the Biochemical Analysis of Genetic Variation

Arti Singh et al. Nucleic Acids Res. .
Free PMC article


Understanding how genetic variation affects the molecular function of gene products is an emergent area of bioinformatic research. Here, we present updates to MutDB (, 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.


Figure 1.
Figure 1.
SNP query tool snapshot highlighting SNP filtering. Multiple filtering options include: validation (T/F), HapMap (31) (T/F), Location, avHet, avHetSE, HapMap Frequency (CEU, CHB, JPT, YRI), SIFT score and UCSC conservation. Users can preview current filtering criteria by scrolling over pop-up window link. Once SNPs are selected, Haploview like images can be rendered showing HapMap LD structure (lower right).
Figure 2.
Figure 2.
MutDB-KEGG integration example of the VEGF Pathway. This pathway shows all proteins with SNPs or Swiss-Prot mutations and all unique diseases and comments provided by Swiss-Prot (top). The VEGF signaling pathway showing proteins with mutations in yellow (bottom).

Similar articles

See all similar articles

Cited by 17 articles

See all "Cited by" articles


    1. Mooney S. Bioinformatics approaches and resources for single nucleotide polymorphism functional analysis. Brief Bioinform. 2005;6:44–56. - PubMed
    1. Ng PC, Henikoff S. Predicting the effects of amino Acid substitutions on protein function. Annu. Rev. Genomics Hum Genet. 2006;7:61–80. - PubMed
    1. Ng PC, Henikoff S. SIFT: predicting amino acid changes that affect protein function. Nucleic Acids Res. 2003;31:3812–3814. - PMC - PubMed
    1. Sunyaev S, Ramensky V, Koch I, Lathe W., III, Kondrashov AS, Bork P. Prediction of deleterious human alleles. Hum. Mol. Genet. 2001;10:591–597. - PubMed
    1. Yue P, Melamud E, Moult J. SNPs3D: candidate gene and SNP selection for association studies. BMC Bioinformatics. 2006;7:166. - PMC - PubMed

Publication types